Many thanks to the Rabbi for his quick reply. In truth, that was indeed my intention: that of course there must be a command and warning, and the only issue is what the punishment comes for—whether for the very act of transgression itself, or for his being a sinner and rebel in having violated God’s command. Although at first glance it seems from the Sefer HaChinukh, commandment 69—which I learned from what you wrote in the references above, and thanks for that—that there can be a punishment for a sinful act even without a command; except that the Torah wrote a command regarding every transgression in order to inform us that this is His will, may He be blessed, and not just a bare transgression with a punishment attached. At least, that is how I understood his words.
What the Rabbi brought from Maimonides in the ninth root principle—I also noticed that. But what you wrote, that he transgresses only one prohibition, is not precise, because if so, what have we gained in proving from this? In Maimonides it is explained that even though the Sages said that he transgresses several prohibitions, nevertheless he is lashed only once, for they did not say “he is lashed for such-and-such and such-and-such.” And this proves that the transgression is one—that is, one undesired matter—and the multiplication of prohibitions and warnings is only to reinforce the matter. Even though he violated several warnings, still he is lashed only once, and this proves that the punishment of lashes, at least, is for the transgression itself and not for rebellion against the command.

What we were taught in the yeshivot is as follows.
Now, Maimonides’ well-known statement is that the prohibition itself is established by one witness. The Penei Yehoshua asked: how is this different from a father who is believed to say, “I betrothed my daughter”? The Torah believed him for prohibition, but not for execution. He asked: but the prohibition itself is established by one witness, and once we establish her as a married woman, then anyone who has relations with her should automatically become liable to stoning.

Rabbi Akiva Eiger, in Tinyana at the end of responsum 107, wrote that perhaps one can distinguish between lashes and death, though he did not explain the distinction. Later authorities wrote—Zekher Yitzhak, sec. 46, and Kovetz Shiurim on Ketubot, no. 58, in the name of the Gaon of Valkemir—that the law of death is different from the law of lashes: lashes come for the prohibition and the negative commandment, whereas death comes for the reality that he had relations with a married woman.

And it seems to me that there is some difference between the definition in Kovetz Shiurim and that in Zekher Yitzhak regarding the “object/status of prohibition” in capital offenses: whether the factual existence of the prohibited object/status is enough even without an actual prohibitory command—and that is apparently the view of Kovetz Shiurim—or whether we require an object/status of prohibition together with a command, and only the death penalty does not come for rebellion against the command but for the prohibition of a married woman, not merely for the bare reality of a married woman without a prohibition, as seems implied by Kovetz Shiurim.

The source for saying this is the language of the Torah itself. With lashes, the rule of lashes is not stated separately for each and every transgression; rather, for all transgressions only the prohibition is stated, and we derive the punishment for all the Torah’s prohibitions from the prohibition of “You shall not muzzle an ox while it is threshing,” where it says “he shall be struck forty times,” etc. By contrast, with death penalties, for every transgression that carries liability to death, the death penalty is stated separately.

And see there in Zekher Yitzhak, where he proved this from the passage in Temurah according to Rava, that if one acted, the act is ineffective. And in truth this also seems to emerge from Nachmanides’ glosses to Sefer HaMitzvot, root principle 14, in his dispute with Maimonides regarding whether the punishments of those liable to death by religious court are counted among the commandments, but this is not the place to go into it.

According to this, Zekher Yitzhak explained that one witness is not believed to clarify the factual reality that this really is forbidden fat; rather, he is only believed to establish the prohibition—that it is forbidden to eat this piece and that it has prohibited status. Therefore, whoever eats the piece would become liable to lashes, because even if it is not really forbidden fat, he still violated the prohibition of forbidden fat. But there would be no death penalty based on one witness, because for that it is necessary that he truly had relations with a married woman, and it is not enough that he violated the prohibition of having relations with a married woman. I later saw something along these lines in Avi Ezri, Sanhedrin 16:6.

But on the other hand, it seems from some of the greatest later authorities that they did not take this approach, even regarding liability to death—namely, against what those above held, that death does not come for violating the prohibition but depends on the factual existence of the object/status of prohibition. From the Penei Yehoshua on Ketubot 22b, supplementary notes, sections 71–72, and from Rabbi Akiva Eiger, first edition, at the end of responsum 107, and also from Shev Shema’tata 4:8, it is clear that they understood that liability to death as well comes only because one violated the prohibition. For see there: they hold that majority does not help in capital cases, yet if the majority determination existed prior to the act—for example, where most women are not barren, and we therefore determined that she is a married woman—then one who has relations with her is, in our eyes, established as someone who violated the prohibition of intercourse with a married woman, and he is liable to death for that. See all their formulations there on this matter. So it emerges that they hold that both lashes and death come for rebellion against God’s command and for violating the prohibition.

On the other hand, in Ketubot 32b we find that Rabbi Yohanan did not say like Ulla, that in a case of lashes and monetary payment one pays and is not lashed, because if so, “You shall not uncover the nakedness of your sister” would be nullified—in a case where one raped his sister, for rape incurs a monetary fine. And Rashi explains: the punishment for the prohibition is lashes. We see from this that a prohibition without punishment is deficient in the very prohibition itself, because it has no meaning to say that one can violate it without receiving punishment for it. And if the punishment is an external matter detached from the body of the prohibition—namely, for the rebellion of the person, while the command is only the occasion for rebellion—then it is not understood why “You shall not uncover the nakedness of your sister” would be nullified, since the prohibition exists in its own right even without punishment. True, this is difficult in light of prohibitions involving no action and prohibitions repaired by a positive commandment, which have no punishment and yet still exist as prohibitions. Tosafot indeed asked this and explained the Talmud differently, but Rashi does not seem to follow Tosafot, rather as above, and so it remains difficult.
All this has brought me to a state where the matter is not clear to me in truth.

It’s hard to address all of this, and it would require a lengthy treatment. So I’ll try to say something briefly.
Maimonides’ view (against Tosafot) is that violating two prohibitions does not mean being lashed twice. And that is exactly what I meant: from here we see that one is lashed for the prohibition, not for the command (there are indeed two commands, which for Maimonides are two prohibitions, and nevertheless one is lashed only once). According to Tosafot, who hold that one is lashed twice, one could perhaps discuss whether the lashes are for the command (though even according to their view, where it is not stated that this counts as violating two prohibitions—such as repeated mentions in Scripture of the prohibition of labor on the Sabbath, which are not counted at all, neither for prohibition nor for punishment—certainly one is not lashed).
As for Maimonides, there are other possible resolutions. For example, that the credibility of one witness is absolute in matters of prohibition, but the father’s credibility is not absolute from the outset. And plainly this is because his credibility is only due to practical necessity. Who else would be believed if not the father?! But he is one witness in a matter of forbidden sexual relations, and he is a relative, etc. Practical necessity requires us to believe him regarding the factual situation, but not regarding punishment, where we remain with the basic law. By the way, many have already questioned this whole principle—that a prohibition is established by one witness—from various sources (including within Maimonides himself), but this is not the place.
Bottom line: to build such a large conceptual edifice on this slight question is, in my opinion, mere pilpul.
However, specifically regarding a married woman, there may perhaps be room for this line of reasoning (that the punishment is given for the transgression and not for the command), as I explained in my article on the guilt-offering: the prohibition of a married woman is a prohibition generated by reality, not by command. See there carefully:

מהותו של קרבן אשם

And the difference as to why with lashes the punishment is not stated separately in every place is only because of quantity. There is no need to resort to any essential, principled distinction between them. Especially since in several places in the Talmud and in the medieval authorities regarding death and lashes we find “What difference is there between complete killing and partial killing,” and they also made various other comparisons between them for several matters. And the plain sense is that they are of the same kind, differing only in degree. Likewise Rabbi Akiva Eiger in Makkot, on page 5, who disagreed with Tosafot regarding liability to punishment without a religious court ruling, did not distinguish between lashes and death.

Many thanks and much appreciation for your brief reply. We would be very happy to hear a fuller treatment of the matter at any other time and place.

As to your actual points: if possible, could you point me to the Tosafot you mentioned? And why did you write that according to Tosafot there is room to discuss it—isn’t it actually necessary? For if not, why is he lashed several times, seeing that he performed only one act, and only once?

If I understood correctly your rejection of the proof from Maimonides about “the prohibition being established,” your intention is that one could say that both in prohibitions punishable by lashes and in death penalties the punishment is for the factual reality of the transgression and not for the negative commandment—and not the other way around? Or do you mean that the issue is open both ways?

I did not understand what you wrote, that in matters of prohibition the witness is fully believed even regarding punishment. If so, why can’t we punish someone for eating forbidden fat by means of one witness who testifies that he ate forbidden fat? And if he has no credibility for punishment regarding a prohibition, then how in the case of an established prohibition is he fully believed even regarding punishment?

And I also did not understand what you wrote, that a father is believed about his daughter because of practical necessity, etc. Why is there no possibility of witnesses for these betrothals? And further: if there is no alternative, then let him not be believed at all—after all, this is a matter of forbidden sexual relations.

What you wrote about the number of prohibitions—are there more prohibitions punishable by lashes than death penalties? Even if there are many, have we found that burden of writing is a reason not to write something in the Torah, with no substantive basis in the matter? And what counts as “many”? Even among death penalties, aside from the types, there are many capital offenses written separately.

I did not understand the proof from the comparison between lashes and death regarding the body’s receiving the punishment. What does that have to do with the reason for the punishment, such that they must be equivalent? This needs expansion and evidence.

I don’t currently have time to elaborate on all this. A few quick points.
According to Tosafot, he is lashed several times because he violated several prohibitions. But these are several prohibitions, not merely several commands. For example, interest and usury are violated in the same act, but these are genuinely two different prohibitions: increasing the lender’s wealth and biting the borrower, as Rashi says at the beginning of “What Is Usury.”
The Tosafot, if I remember correctly, is at the beginning of “What Is Usury,” where he asks why it helps to multiply prohibitions if there are no extra lashes. See my article “And It Sent Forth Its Roots.”
The question of what the Torah writes and what it does not write is not simple, and it is hard to learn much from it. As is known, Rabbi Eliyahu of Vilna learned from the Torah’s lengthiness regarding Eliezer (“The conversation of the servants of the patriarchs is more pleasing…”) that length determines importance. But that is not so. Regarding murder, for example, the Torah is very brief. And in general there are mountains hanging by a hair.
If there is a difference between lashes and death, one cannot learn from one to the other. Just as we do not derive monetary law from prohibitory law, and the like.