If you think a deep-dive on hylomorphism is going to end this debate, you don’t really understand what you’re talking about.
Thanks for the post! I have a question, and since I am about to do a "deep dive on hylopmorphism", I am more than happy to admit that I probably do not know what I am talking about! Regarding the statement from the diocese that biological sex cannot be changed: are we entirely sure that this was intended to be a scientific statement? It seems to be referring to form, held in the intellect. Whether or not the matter can successfully be artificially re-arranged to function like the opposite sex is perhaps the question for science; but whether or not the form and essence of what it means to be male or female changes along with the matter is a question that seems within the realm of the Church. My understanding is that form informs matter, not vice versa. Even after death, when the body of a person becomes a corpse and decays, the form of the deceased human is preserved in God's intellect and not in the matter, and it is this form which again takes on matter in the resurrection of the dead. Or at least this is my understanding.
I think you're point about delineating between that which is a theological question and that which is a scientific question is really helpful. I have no answer to it, but I do wish to raise the point of how this connects to a certain part of Thomistic (and concomitantly Catholic) understanding of nature. Typically, Natural Law when appealing to nature makes a difference between that which is intended in nature and that which is incidental in nature, with that which is incidental in nature a result of the fall. One could reasonably interpret from the genesis line "male and female he made them" that that is talking about the intendedly natural, and from this that the transgender experience is rather that which is incidentally natural. but intended or not, this has no bearing on a reasonable, and scientific, observation that the transgender experience does exist, and we still have to deal with this in some meaningful sense (as the church had done with hermaphrodites in the past). And we can't merely appeal to that which is intended to solve that which is merely incidental. For example, whilst one might consider paralysis from the waist down as being incidental in nature, we do not from that insist that paralysed people just walk - we continue to provide them whatever care they may specifically need (e.g: use of a wheelchair). Use of a wheelchair is not a rejection of what was intended in nature (non-paralysis), but rather an recognition, and a practical accommodation of that which is incidental in nature (paralysis). So if we apply the same to the transgender experience, whilst one could argue that it is not intended in nature, it would be naive from that to a) deny people's genuine experience of gender discordance and/or dysphoria and b) insist that such people do nothing about that experience, and just try to pretend they are the gender that they do not identify with.
The scientific approach addresses that which is, and the theological that which was intended. Even if we can create a fully comprehensive theological analysis of what was intended, that does not necessarily allow us to answer how we should deal with that which is. The question at hand is how do we deal with that which is, and simply appealing to that which was intended does not necessarily provide us with an answer to this.
This comment is rather ragtag, and I have not fully organised this in a comprehensive cohesive way, and nor do I answer many of the questions you have raised, nor those which I have. But I hope that some of my insights here may be useful.