"A bunch of Yes/No choices at the start, or ask each time a [insert Tag] scene come up?"
None of this. You're a writer, use your story to know what the player want, then keep track of his answer to know what content you should present him.
Something that would looks like:
Code:
MtF "I started taking hormones just one year ago, what mean that technically I'm still in the middle of my second puberty. But, you know, my boobs are already not so bad."
menu:
"I prefer vaginas.":
$ transContent = False
$ MtF = False
MC "Don't take it wrong, I have nothing against transgenders, but I want my girls to have a vagina, not a dick."
"You're a good friend."
$ transContent = True
$ MtF = False
MC "You aren't trying to seduce me, are you ? You're a too good friend of mine, I don't want to loose you over a question of sex."
"Pict or it don't happened.":
$ transContent = True
$ MtF = True
MC "I'll believe you when I'll see them."
And when it's not possible to wait for the right moment, like by example when you want to present a story where a character is either MtF or female, still try to insert it into the story.
At the early stage of the game, make the MC have a discussion about transgenders with his best friend (about that girl in school, that new co-worker, or that celebrity). Or, why not, making the player buy a porn magazine and have to choice between one that have females and MtF, and one that only have females.
99% of the time, it's possible to do this through the dialogs, therefore do it that way. Prove to the players that you correctly handle your writing and don't need to throw blunt questions to make it advance.
As for the 1% when it's not possible, try to make it as invisible as possible. By example by making the MC have to fill a really weird medical form by example. It will be a bunch of yes/no, but at least it will fill natural and part of the story.