There is no report or evidence of brain damage. Only soul damage, which was repaired by splicing in a male soul.
Now if you want to take the position that souls don't have gender, or don't exist, then you can argue with The Creator - the artist/author who defines this fictional world and is the absolute final authority thereon. (Hint: you lose.)
So if souls have gender, and the only soul-gender Natani has any contact or communication with is male, but Natani's body is female, then in what sense is Natani not transgender?
You could argue that Natani's soul was not as damaged as thought, and the original condition is reasserting itself. You might have a point on that... but based on the available evidence I would tentatively say that Natani was originally gender-neutral or genderfluid (or both), not female. And the combination of that condition with the splice and the healing process could quite possibly land him at a condition of being merely less paranoid about his female body (but still clearly transgender).
Now if you're objecting to a certain tendency to toss everyone who isn't solidly cisgender into the "transgender" bucket... that, I agree, is belittling to genuinely transgender people. And I'm mildly genderfluid myself, so I have some idea whereof I speak; if nothing else, treating the dozen or so less-than-twenty-minute bouts of gender dysphoria that I've experienced as being in the same category of emotional difficulty as living with gender dysphoria every waking moment with no expectation that it will end short of death... no. Just no.
But it seems a pretty solid case to me that Natani was transgender, and I haven't seen anything yet that definitely says he isn't transgender.