@hungry: A thoughtful post. Some of your questions invite more philosophising and rumination than I feel like I want to commit to, so I figure I'll just do you the unfortunate discourtesy of zeroing in on one part.
You ask: 'If one feels that they should have their gender and sex coincide, is it more right to change their mentality, or change their physicality?' There are two things I take issue with here. The first is the notion of doing what is 'right' with regards to your gender identity. I don't think it's healthy or productive to bring morals into a debate like this, and while I doubt this is what you were doing, from experience I have come to believe that many people do make a moral judgement which says that others shouldn't change their gender physicality. Perhaps out of libidinal discomfort with the idea of gender uncertainty, I have seen people treat the idea of transgenderism as disgusting, repulsive and reprehensible. I'm not entirely innocent of this; as a man myself, I would not want to sleep with a trans-woman (and I apologise if that upsets any trans-women reading this, but I promise you're not missing anything). However, that does not mean I see them as inferior people or having made the 'wrong' change to themselves. Talking about it in terms of moral 'rightness' only encourages marginalisation of a group who are evidently already struggling with difficult choices.
You may of course not have meant moral rectitude but instead been talking of scientific 'rightness' - as in, taking the course that medicinal science would most likely prescribe in order to produce a healthy outcome. This leads me on to my second problem with the question, which is with the word 'mentality'. To my layman's understanding, there is little scientific doubt any more that male and female brains have marked differences. Exactly what differences, how much they account for gender identity, and the question of when does a male brain become a female one or vice versa, are all, I understand, still unclear. Every year some babies will be born with genital defects or no genitals at all. These babies are often reassigned gender at birth as part of surgery to help their excretory systems. Despite being raised as a certain sex, they frequently (8 out of 14 subjects in one study) come to identify as the opposite. There's also the famous case of David Reimer, a man who in his childhood had been raised as a girl after a botched circumcision. His case was presented as an example of the theory of 'gender neutrality', until he came to re-identify himself as male in his adolescence, then later killed himself after years of depression.
These cases suggest to me that the mental aspect of gender falls more into the category of unchangeable 'neurology', rather than 'mentality', which has the connotation of being something much more easily changed. Studies seem to agree, to the degree that neurological sex sometimes appears to match a person's professed gender identity while not matching their genetic sex. 'Physicality' - at least in terms of the genitalia alone - actually becomes one of the more minor parts of the gender puzzle when considering things in this light.
While I agree that berating the opposition is not the best way to win anybody around, it does seem clear to me that in this particular debate there is one stance which has the potential to upset and hurt members of a minority community and another stance which supports them, the latter in turn being supported by a solid body of research data. (I'm also linking in @rangers517 since he asked a related question).
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