Answer

Hello.
I’ll begin by saying that in my opinion, commentators on aggadic literature usually deal with it in an unconvincing way, so I generally do not involve myself with it or with them. It is usually just clever homiletics and pilpul.
I would also note that the Talmudic passage you cited is itself difficult. After all, the verse it brings says to Moses our teacher, “Do not continue speaking to Me… Go up to the top of the mountain,” meaning that he is specifically being told to stop his prayer so that he can go up to the top of the mountain. So why is this verse proof that prayer is preferable?
And in fact, Rabbi Eliyahu Mizrachi Horowitz inferred from Rashi that the lesson from the verse is different: the verse says “about this matter,” meaning that only by virtue of this matter (= prayer) was his request partially answered, and he was told to go up to the top of the mountain. The prayer is not what the Holy One, blessed be He, is telling him to do now, but what he had already done, and by whose merit he was rewarded. As I said, this fits the plain sense of the Talmud much better. But Tosafot really did not understand it that way, and their words are difficult because of the very reliance on the verse. It seems they understood that the Holy One, blessed be He, is instructing Moses to pray.
As for the question on Tosafot itself, in my opinion it is not really a question. Tosafot only comes to sharpen the logic of the Talmud and show that although Moses had good deeds, prayer was still required of him. We therefore see that prayer (which he would do now) together with deeds (which he already had to his credit) is greater than deeds alone. But that is trivial, so Tosafot clarifies and sharpens the point: the Talmud’s intent is not that, but rather to teach that prayer alone is greater than good deeds alone.
How can that really be learned from the verse, if he had both good deeds and prayer? Tosafot sharpens the point that the Talmud means to show that the comparison is between prayer alone and deeds without prayer. And it proves this from the fact that Moses was told to pray instead of continuing his deeds, and from here it is clear that the addition of prayer is more important than the addition of the deeds he would have done at that same time instead of praying. From here it follows that prayer alone is greater than deeds without prayer. But as I said, all of this is difficult in terms of the plain sense of the verse.
As I explained, the question on Tosafot is, in my view, not really so difficult, because they are explaining the plain sense of the Talmud. But indeed, the plain meaning of Tosafot is that they understood the Talmud to be comparing prayer without deeds to deeds without prayer. And the proof from the verse is as I explained—regarding the immediate moment, whether it is better to continue doing deeds or to pray.
He explains that Tosafot’s intent is to teach that the comparison is between prayer together with deeds and deeds alone. And you are right to ask that this is trivial. There is a novel point in Tosafot (to exclude the initial assumption that the Talmud compares only prayer to deeds alone), but in the Talmud itself there is no novelty at all. Therefore it seems to me as I wrote above, and not like his explanation.