The General specifically said (to paraphrase) "I'm back to normal am I? that was the only time I've been a man - cringey fauxmenist comment about men's egos." And I think that that was a very specific choice to canonically squish the arguments about "why would the Doctor randomly become a woman after 13 male regenerations?"
As for the gay/trans thing - if they're attracted to people of their birth sex, then they're straight. Because on the whole people of their assigned birth sex will be of the opposite gender to them. It's a little confusing because the language has not yet adapted to accommodate trans* people. But anyway...
You're right that now that the Master has changed genders you could construe that as evidence that she's identified as a she all along. But prior to that there's been no evidence of that that I am aware of. You're using the benefit of hindsight. "Well clearly Missy is trans* because she changed genders, but the Doctor obviously isn't because he has never changed genders." Even though up until last year the Master's gender situation was exactly the same as the Doctor's. I.e decades of multiple, male only regenerations.