How so? Male and female brains have the same differences between each other...does that make one or the other a 'mental disorder?'

And of course the studies examine a few very specific brain structures- those are the few specific brain structures that differentiate naturally between males and females.

Where are you finding that 'the VERY concept of male vs. female brains is highly controversial in the first place'? Just a quick google search lead me to three medical and two psychology sites that state the male vs. female brain structure differences very matter of factly.

Also, in this sentence:

...these studies have only shown these differences many YEARS after the behavior occurred (and usually with hormone treatment or surgery occuring)...

What behavior are you referring to? You seem to differentiate between said 'behavior' and the use of hormone treatments and surgery, suggesting you mean something different than those two things.

What behavior do you think is occurring- besides hormone treatment and surgery- that is literally changing the structures of these people's brains? Come to think of it, I understand how hormone treatment could, but how would surgery on any structure other than the brain actually manage to change the brain's structures as well?