Sorry if this seems nit picky, but I don't consider the Comic Relief spoof to be canon with the TV series
Oh I don't either. I just thought of it as an actual example of a female Doctor onscreen. And the Doctor barely blinks, just looks at her Companion (that she's engaged) and wonders if the'll both wear white. It doesn't bother, not fazes her.

Ditto Eleven - he thinks he might have become female, as if this is something perfectly logical. (Generally, then he has so little regeneration control, I have no problems with him ending up female... There'd be no conscious choice involved.)