I concur with what annie and RP have said.
It's a shame that S did this unthinkingly and while under the influence, especially as you said you and she had one poly thing that ended badly and then she had another relationship that was bad from the start. Seems to be a pattern... ugh.
Life is complicated enough with all those rugrats you all have got! Fucking roommates is very dicey... Fucking couples is also complicated as hell. Triple complications!
I do wish you and S well. You've been kind to take in some internet friends. It's a shame they didn't think to make sure you were OK with them having sex with your partner.
S's gender transition doesn't seem to be all that pertinent here, but I just wanted to let you know, my partner is also MtF trans. We've been together 3 years and she'd started fully transitioning just a few months before we met, so I know what you mean about a 2nd adolescence. It's hard work for her, and for you.