I started a game with
Same Sex Couples and LGBT Families for my new playthrough of Killer Frost. It worked in the intro pretty well. I was not thrilled with the face that was used for her spouse. But that was easily changed in character generation by using a Looksmenu preset. I actually used Annie Ley Oak's face!
When playing the Female-Female version, your character has to be the second person in front of the mirror. Basically just like the vanilla game, you have to use the change sex option to go to your character.
What is a little odd that both wear the same outfit to start with. You can use the console to change the clothes of either (I never thought of that until later). But once the news announces the start of the war, your spouse magically changes clothes to
jeans and white tee shirt. It would have been nice if they had just started that way.
I added some mods after my first night of playing. Then went back again a day later. I found that my character was now male!

As far as I can tell, none of the mods I added had anything to do with the original spouse's sex. It was stuff like crafting items. Just out of curiosity I tried disabling Same Sex Couples and again when restarting my character was male. Finally I activated the mod again and just moved it down the load order, and Frost was magically female again.
Edit to add:
I found an incompatibility between
Remove Scope Sway and
Same Sex Couples. I never would have imagined it, but each completely cancels the other out. Whatever loads last wins, and disables the other.
I looked at Remove Scope Sway in the CK, and I think I see why. It adds a perk that stabilizes your aim. Then it adds that perk directly to the Player record. I expect that Same Sex Couples also directly modifies the Player record. So there the the problem.
The upside is that deleting the Remove Scope Sway perk from the player record via FO4Edit and making it completely standalone should work. Then you could simply add the perk via the console. Or with a quest.
I found another incompatibility.
Same Sex Couples and
Revamped Playable Ghoul Mod do not work together. If you have Same Sex Couples on, your ghoul character loses their ghoul textures.