There is no misunderstanding about the meaning of male and female, the problem comes with the interpretations by those affected with a condition, be it physical or psychological in nature.
You can call yourself whatever you want, but when doctors bring a baby into this world, I assume they expect to be told is a boy or is a girl, not some gender unespecified blob with a couple of tiny balls.
Did you just assume the gender of my baby? Hilarious, he/she might choose whatever in the future, but most of the time, is pretty clear to all involved, if it were not, then there's your condition.