you raise a good point, a really good point actually.
It does seem very strange to me that LGB people are somewhat more "accepted" although there is no medical backing to provide evidence for why they identify sexually the way that they do. Whereas as you pointed out, for those who are transgender, there is medical evidence/chromosome proof of different causes for transgender variations.
I think it boils down to the fact that the average person can more easily understand a lesbian/gay/bisexual person better than they can understand one who is transgender due to the complexity. What people don't understand...they're often ignorant of.