Also not an SO, but I can tell you how mine has progressed.
I was seeing a very hetero woman and eventually came out to her because my mood swings over suppressing this were starting to affect the relationship and I didn't want to lose the ability to keep her as a friend if she wasn't okay with it. It turned out she was okay with it, but things changed and although I'm sure she had thought things through, I'm not sure she was as prepared as she could have been.
We're still together and married with 5 kids. I think this is where your situation differs and it can be significant if you want kids still, but there is hope. Your SO can turn to storing their sperm for future use. The hormones affect different people differently. My sex drive went from 10 to 0. For some, it increases. I believe for all, sperm production stops after several months, so it would be important to store it first.
I'm on HRT and full time. I can still enjoy sex, but I don't get in the mood anymore without already being in the act. This has caused some issues for me personally because she ends up not getting her needs fulfilled and when I try to do it anyway, it turns into an argument about how wrong it is for her to do that if I don't like it. So we kind of go back and forth between her needing it and her not wanting me to fake it. I liked women before starting and that has not changed. It's just primarily on an emotional level now.
I'm sure you've thought all of these scenarios through, but you'll want to make sure you have support, aside from your SO, to deal with them as they arise. Love is love works great, but eventually the world that's been crashing down on your SO is going to come for you too. People treat her differently now because they see us as a lesbian couple. We don't do any PDA, but people still see it. She's lost friends and family over supporting me too.
Communicate, communicate, communicate! I can't stress this enough. Your SO will be going through teenage girl mood swings for a bit and she won't realize how snippy she's getting. When that happens, the tiniest things could be blown out of proportion quickly, so make sure they're communicated as soon as possible, from both of you!
The community needs more SO support groups too. She also is dying to have other people to talk to about all this. She says she's even more of a minority than I am and she's right. She's not gay or bi, but she's being treated like she is because she loves me and it's getting to her. She's finding people she's known her entire life are anti-trans activists and having to deal with pushing lifelong friends out of her life. Taking her to therapy with me helped, but she really needs a way to speak to someone about all this without me in the room.
It does work though. She's as much my own support pillar as I am hers. She builds up my confidence to levels I've never known and I make sure she knows how much she's loved and appreciated.