It is true that we have a similar brain structure and represent all but a mere point in the endless space of mind design possibilities, but there is a lot of variation within that point. Just think about the variables in operation over here. Billions of neurons with multiple connections in a chemical soup, firing in a patter and changing while sharing information.
It isn't surprising that we don't understand this, but you'll be amazed at the psuedo-science out there did you know that there was something called Oppositional Defiant Disorder (see: http://www.minddisorders.com/Ob-Ps/Oppositional-defiant-diso...)? I cannot name one scientific, unbiased experiment for the root causes behind expression and functioning in gender variant, or intersexed children.
There is some amazing work being done at the national institute of mental health in the underlying neurological basis of mental health disorders like depression and PTSD, but it isn't enough. (see: http://www.scientificamerican.com/article.cfm?id=faulty-circ...)
The disappointing thing is not the lack of knowledge but the psuedo-science out there and the self proclaimed experts willing to ruin lives without a flinch. We've come a far way, but we have even farther to go.