1. I wish our medical technology was at the point you seem to believe it is, I
truly wish it was. But it's not. I wish society was at the point it is in the Culture series, where every individual in the Culture has the ability to change their biological sex at will (and even become androgynous if they wish!). But we are certainly not at the point. Post-op transwomen
don't have vaginas, just as they have none of the other plumbing that exists as part of being one half of a sexually reproducing pair. They have imitations of them, poorly reconstructed from, yes, as you say, a mutilated penis. I hope that one day (sooner rather than later) we will get to the level of medical prowess where this is not the case, but we are certainly not there in 2021. In the same way, I hope that one day soon we will be able to make legs for people that lost/never had them (if they wish). Offense is taken, not given – it is not that I don't understand that people can be offended by "intact", it is that someone taking offense at an accurate description of reality is generally not worth the effort to guard against, because with that low of a bar people can be offended by
anything. But again, I already agreed not to use that terminology, which (again) I was only using in the first place because it had been used previously in the conversation without objection by someone else.
2. Two-spirit was a term invented in 1990, so that seems like a bad example of a concept that has existed throughout history. Even the concept of a "special third gender" necessitates that you have two primary ones. I am not arguing that every society throughout history has had two distinct gender roles and that is all. The point I am making is that the reason gender exists as a concept at all is because there are distinct human sexes. The reason there are distinct sexes is because that is what we are: a sexually reproducing species with binary sex characteristics. One sex that produces the large gamete and one sex that produces the small, which come together to form zygote, which is incubated by the aforementioned large gamete provider. If it worked in any other way, if there was any variation on this theme, you and I would not exist. Your progeny involves one male having sex with one female and the female carrying the result of that in her womb for at least 20+ weeks (usually 40) in an unbroken line back to the first human, and then much, much further.
3. I never claimed men were uncontrollable rapists, just that the statistics (to the best of our ability to measure them) indicate that rapists are far more prevalent among males than among females. Clearly the vast majority of men are capable of not raping people. Furthermore, "rape culture" is a strange way of describing a culture which has harsh punishments for rapists and frequently makes people unemployable after the mere accusation of rape, with little proof needed (name another crime we do that for as readily). In fact if I was going to invent a "rape culture" from scratch those things would definitely be the opposite of what I'd include as norms.
Look, if you want to dismantle the prison system because it normalizes and perpetuates horrible violence, then by all means say that. But this is not at all the same thing as saying "we can just stick people in whichever prison best matches their gender identity regardless of what reasons we had for making men's and women's prisons in the first place because clearly the people who made that decision were poorly reasoning morons/bigots who had no reason to make such a distinction". Just as saying "we should develop more gender-neutral bathrooms" is different from saying "men and women's bathrooms are functionally identical just with different signs on the doors", even though men's bathrooms were clearly designed around the assumption that users of said bathroom are likely to have a functioning penis.
I personally think that we as a society should move away from gendering everything in general. Bathrooms, clothes, toys, prisons, makeup, etc. could all be much more gender neutral than they are and I think that would be a good thing. Until then, when talking about interim solutions, "are we throwing the baby out with the bathwater" is a valid question.
Justice for everyone is inseparable from justice for anyone.