The first creature that developed sex chromosomes would seem like they had a disorder compared to what they descended from, so we are all disordered
First off, there are some people who are both with both male and female genitalia. Second, we don't know enough about the brain to tell if the mind isn't constrained by biology in that way. After all, our mind is made of the very physical and biological neuron pathways.
Someone who is trans could very well have a brain structure more similar to someone of the opposite gender. We do know that there are differences between female and male brains, based on differences on how autism is expressed in different genders. The brain is incredibly complex and more research is needed.