you fail to distinguish between the question of whether to let people self identify themselves and whether people in hormone therapy really change their gender.

Well, I may or may not be mindkilled but I'm certainly confused. The only mention I made of hormone therapy was to suggest that in the special context of prisoners wanting to move to a different prison on account of gender transition, being on hormone therapy might be a useful criterion for being demonstrably serious. (Not for being actually male/female. The point is that it is evidence of the sincerity of the prisoner's claim, which we need because in this situation insincere claims might otherwise be a problem.)

So far as I can see,

the debate whether or not an XY transsexual with no penis, a vagina and big boobs is female or male

simply hasn't come up in this discussion, or at least not the bit of it you and I have been engaging in. Accordingly, I have no idea how anything I've written can suggest that I'm failing to distinguish that debate from any other debate. I also don't think the question was ever quite

whether or not the act of identifying as female means that your gender is female.

although obvious that isn't a mile from what Fluttershy was saying.

So it looks to me as if there's a failure of communication here. Let me attempt to say clearly and explicitly what I think the issues are. My apologies for the length of what follows.

• Underlying question #1: under what circumstances, if any, is someone who is anatomically/chromosomally/hormonally male "really" female?
  • I'm not sure this is the sort of question that has a definite answer. There are multiple somewhat defensible ways to use words like "male" and "female" and the answer could be different for them (even without bringing transgender into it; intersex conditions are pretty complicated).
• Underlying question #2: how should we use terms like "male" and "female" in cases where there's divergence between those features and others such as the person's (expressed and/or internal) "gender identity"?
  • My own opinion is that we get a healthier and happier society by usually taking "gender identity" as having priority over anatomy, chromosomes, etc., and accordingly that if someone identifies as (say) male then in most contexts we should treat that person as male.
  • There are plenty of exceptions. Your example of prison might be one. So might competitive sports. So, for sure, might medical care.
• Fluttershy's proposal was to answer question #2 with "according to expressed gender identity".
  • Fluttershy didn't say anything about difficult cases where there's ground to suspect that expressed and internal gender identity might differ (e.g., someone trying to exploit the system), where taking someone at their word might be more than averagely dangerous (e.g., when the person in question is a violent criminal), etc.
  • One possibility is that Fluttershy simply believes we should always, unconditionally, take everyone at their word on this issue. I think that is unlikely; in any case, if so then I disagree. (See above.)
  • Another possibility is that Fluttershy was proposing a general policy, which might need modification in unusual cases (e.g., prison), but stated it briefly without all the caveats that it might need.
  • My money is firmly on the second of these, and in particular I am fairly sure Fluttershy was not saying that the mere act of saying "I am a woman" makes someone a woman.
• Your response, though, was to point to an unusual case as if it demonstrated the badness of Fluttershy's proposal.
  • If you were taking Fluttershy to be claiming that we should always, unconditionally, take everyone at their word, then I think that is a needlessly uncharitable interpretation, enough so that I will gently suggest you consider that I might not be the only person in this discussion vulnerable to politics.
• I pointed out that "hard cases make bad law"; that the fact that a policy of always taking people at their word might work badly when the people in question are serious criminals is little objection to a more reasonable policy of generally taking people at their word, while being more cautious in some special situations -- like prisons.
• I made some concrete proposals for safeguards one might apply in prisons. As you say, those safeguards mean that we would not be simply and naively taking prisoners at their word as soon as they say "I'm a woman". They do, however, go a considerable way towards accommodating transgender prisoners.
  • That doesn't mean that I regard the proposal with the safeguards as giving a sensible criterion in less dangerous situations. I don't.
• One remark about the context for all this. Fluttershy was responding to a comment from VoiceOfRa which takes it for granted that what's going on with transgender people is (and I quote) "delusions and hallucinations", on a par with someone who believes himself to be simultaneously Jesus and John Lennon.
  • I suggest that it is not reasonable to take Fluttershy's comment as meaning that the whole debate here is between "a person's gender is whatever they have most recently said it is" and everything else, any more than it is to take VoiceOfRa's comment as meaning that the whole debate here is between "a person's gender is determined by their chromosomes and nothing else" (or whatever, in fact, VoR's position is; if he's made that clear, then I haven't seen it). One comment was a response to the other. And my comment was attempting to address both.

that you simply want to be pro-LGBT instead of engaging with detailed arguments that distinguish different questions.

Well, you're entitled to your impression. I confess I'm unsure how you got it. In particular, I don't see that you made any such detailed arguments; in fact, the principal point of my original comment was that you failed to distinguish between "what should we do in general?" and "what should we do for the more difficult and dangerous case of imprisoned criminals?".