This is a perceptive question. I see, though, that you only asked in the Ika d'Amri. So it sounds like you did not find difficulty with the Gemara before the Ika d'Amri.

But if I understand your question correctly, you in fact could have asked earlier as well, for the original question posed was: Is the blood independent or connected? The Gemara asked a number of follow-up questions, including:

1) Even if the blood is independent, does the man just intend to take out the blood, in which case the Be'ilah is Mutar, or does he intend to create an opening, in which case it is Asur?

2) And even if he intends merely to take out the blood, and the formation of the opening constitutes an unintended consequence, still, do we follow Rebbi Shimon that an unintended consequence is Mutar, or Rebbi Yehudah that an unintended consequence is Asur?

According to your line of reasoning, here too, why did the Gemara in stage 2 ask if we follow Rebbi Yehudah? Isn't it obvious from the fact that the Gemara in stage 1 says that if he intends for the blood it is Mutar, that we are following Rebbi Yehudah?

Evdently, the Pshat is that, indeed, originally the Gemara assumes like one side, but later it reconsiders. That is, what was concluded previously really hinged on a tacit assumption, namely, Rebbi Shimon's view regarding Davar she'Eino Miskaven. In other words, not every "Im Timtzi Lomar" is considering a new consideration that is built on top of all the accepted assumptions of the previous steps, but rather, at times, such as in this Sugya, an "Im Timtzi Lomar" is in fact reconsidering a prior assumption and clarifying what would result from adopting the contrary view.

I hope this helps!

Best wishes,

Yishai Rasowsky