Fair enough, Down Syndrome was probably a bad choice. So, let's change it to Autism, or Bipolar disorder, or acromegaly, or blindness. The point still stands, there are people who suffer from different levels of functioning below "perfectly 'normal' and healthy" Brain functioning, and hormones have way more to do with who you are then what you tell yourself you are.
here is another lame example, in my younger years, I went out drinking with some friends. One of my friends fell down a few steps because he was intoxicated. His immediate response was "I meant to do that" Clearly, he didn't, but his brain was still pushing the idea he was in complete control of the situation. I am pretty sure that our brain does its best to make sense of a situation, it acts as if it is control, when really, it is just logging errors.
I need to lose weight, my nephew needs to gain weight. Skinny people like to say "hey have some self control" to us fatty. The reality is, my nephew eats till he is full, as do I. He doesn't get enough calories, and I get too many. Our brains are wired different, the more studies done the more it proves it. I have seen many many fatties loose tens if not hundreds of pounds, just to gain it all back a few years later. When your brain is calibrated a way, it is hard, if not impossible, to change it.
That being said, unless someone was born inter sexed or had some other sexual amorality, I think reassignment surgery should wait till after puberty. Until your sexual organs mature, you don't really know how you will end up. An imbalance of estrogen at 5 could clear itself up by 18.