Actually, a bunch of brain things we thought sorted between men and women turned out to sort between attraction to men and to women, so they won't distinguish a straight transwoman from a cis gay man.

Also, there are quite a bunch of people who transition, then go back, so "it's not a life anyone would wish upon themselves" won't work. I'd much rather trust the brain scanner if it's at all trustworthy (and has a genderqueer slot, thank you very much). If it says "Nope, you're a girl"... well, I'll be seriously disappointed, but I'd make the best of it and be a dyke or something.