Isn't Y Combinator already the Y Combinator for transgendered people? I can't see it affecting an interview or acceptance -- the bathrooms at YC don't even have gender assignment on the door.
My best guess is that, in the mind of this person, her transgender status, rather than the obvious inconsistency and absurdity of her business idea and whatever other red flags she managed to work into her YC application, is what caused YC to reject her.
Yeah, I really think this person would be better off moving to the bay area (which seems to be the plan) and getting a job at a reasonable tech company (where no one cares either way about your sexual orientation, gender identity, etc., except to the extent that you want to get the best candidates to apply/accept, and thus don't want to exclude pools of people intentionally or unintentionally), vs. trying to start an incubator (without money, without any experience or special skills, and in a saturated market...).