Question

This question needs a short introduction, so please forgive the length.
I read the Rabbi’s article on intuition, and a few days later I was learning the Talmudic passage in Yevamot 5a, which deals with the question of how we know, according to the Rabbis, that a positive commandment overrides a prohibition. There the Talmud says that it cannot be that the source for the rule that a positive commandment overrides a prohibition is the case of a leprous nazirite (where, despite the prohibition on a nazirite shaving, he is nevertheless obligated to shave because he is a leper), because if you learn it from there, then it would explain for us where we learned the accepted rule that a positive commandment does not override both a prohibition and a positive commandment.
{“Rather, it is derived from ‘his head,’ as it was taught in a baraita: ‘His head’—what does this come to teach? Since it says, ‘A razor shall not pass over his head’ (Numbers 6:5), I might have thought that this applies even to a leprous nazirite; therefore the verse says, ‘his head.’ But one can challenge this: what is unique about a leprous nazirite? That his vow can be dissolved. For if you do not say this, then that which we hold as accepted law, that a positive commandment does not override a prohibition and a positive commandment—let us derive it from the leprous nazirite! Rather, why do we not derive it from the leprous nazirite? Because one can challenge it by saying that his vow can be dissolved.”}
The Rabbi’s article on intuition made me wonder whether the “kayma lan” of the Sages is בעצם intuition—after all, we have no source for the fact that a positive commandment overrides a prohibition; it is as though it is simply completely obvious to us.
Similarly, we have no explanation in the Talmud of what “kayma lan” means. On the contrary: when the Talmud (Pesachim 2a) discusses the meaning of the word “or” in the phrase “or of the fourteenth” (whether it means day or night), the Talmud suggests saying that “or” means day, and learning this from the verse “And God called the light Day.” The Talmud there rejects this and says that the verse comes to teach that “that which becomes illuminated is called day,” and therefore this is not a proof (see there). About this, the Talmud says that this cannot be, because according to that, from the continuation of the verse you should have learned that “that which becomes dark is called night,” and that is not reasonable because “kayma lan” that the day ends when the stars come out.
Here the Talmud rejects the claim that “becoming dark” (meaning, it is not yet fully dark) could be considered night because it is simply obvious to us that the day ends at the appearance of the stars; it does not reject it on the basis of another source, only because “kayma lan.”
Tosafot there try to explain that this “kayma lan” is learned from Megillah, but in light of the Talmud in Yevamot, where they bring a “kayma lan” that seemingly has no source at all, can one say that “kayma lan,” as a general rule in the language of the Sages, teaches an intuitive halakhic principle that needs no source other than intuition? That intuition itself is enough to understand that a positive commandment cannot override both a prohibition and a positive commandment, and no source is needed at all?
 
Sorry for the length.