I'm not adding anything new ... just reinforcing what everyone else has said, you should find Geneva pretty relaxed (I used to work there, it's a fine place to be!). Because of the large expat/multicultural population there, it's a fairly broad-minded place. I think you're more likely to get unwelcome attention (either for being transgender, or for having a same-sex partner) from conservative expats than from the more numerous local Swiss, who as a rule tend to keep their thoughts to themselves.

What a contrast from the recent "Goth post" (it's not worth linking you to that) -- it's all in the approach. You'll do great here in Switzerland!

With regard to your partner, can you legally get married in some other state, or another country? I would think that could be helpful. Or maybe even in Zurich, as ZuriKT intimated. But don't get married just to get a permit! Sorry, I don't know enough about this subject.