No offense, but this screams bad idea all over.
1) Transitioning is a stressful, messy and complicated process. Trying to start a serious relationship during it is tapdancing in a minefield to begin with. And you don't sound like you want something casual. Add in the fact that you are entirely pre-transition, and she's perceiving you as male... and, like dude, so bad idea. Or to put it another way - chances are this is gonna end in heartbreak (most relationships do), you want that ON TOP of dealing with transition?
2) She's straight. I mean I don't know this 100%. I can't guarantee it. But.. she's straight. Most people are, regardless of whether they harbour hidden fantasies of a same-sex fling. Straight is normal, most people are normal. And straight doesn't work for you and won't work for you. Hell, even the faint chance she's bi is no guarantee. You'll look different post-transition. Just 'cause she was attracted to how you looked as a guy, does not mean she'll be attracted to how you look as a girl. You may become entirely un->-bleeped-<-able in her eyes. Being attracted to girls does not mean being attracted to ALL girls. And pansexuals are so rare they don't even register on surveys outside of queer communities.
3) That she likes pretty boys doesn't imply anything regarding her sexuality other than she is attracted to pretty boys. It doesn't mean she sees you as female. Not even a little. I'm sorry. I was the pretty boy too. That she's androgynous doesn't, sadly, guarantee anything regarding her sexuality either. One of the hottest, dykeyist-looking tomboys I've ever met is married to a bloke with two kids. (So sad.) Yes, there is a somewhat higher chance that she's queer. But the interest she's showing in you is actually evidence against her being interested in you.
4) If this goes badly (and most likely it will). You'll be kicked out of the closet before you are prepared, before you can talk to your family, your friends, your boss, etc. Being outed by someone who probably may not like you very much at that point, who will tell the story her own way (and not to your benefit), is not exactly the best method of coming out. This would be like holding on to a hand grenade with your eyes closed, praying that the pin hasn't been pulled. How well do you know this girl again?
5) It's not just hard to be friends with someone who has a crush on you, it's actually much harder to be friends with someone you have a crush on. That may not be a thing you can or should ask of her. The wanting doesn't generally stop, at least not for a good long while. She may look like a friend after a while, but she's still quietly wanting to screw your brains out. It makes for complicated friendships.
So... ya, this is probably a terrible thing to do. And you should stay way the hell away from this girl. But if you recognize those problems, and you think it's worth it anyway... well, go for it. I did. And it was wonderful and terrible and then it was over. I still don't know if I regret it or not. *Shrug*
(I think I'm the devil.)