Ideas
I've never used CC, briefly used mods but removed them and all of their stray files from my game folder a long time ago.
I also have this problem in CAS. When loading a legacy into a new save, I often have to move the family piecemeal- I move the first 8 onto a lot, move out the majority and only keep the founders, then add the next round of their children and grandchildren- but when the founding couple is same sex, I can only add one of them as a parent and selecting the second parent almost always resets the first to "Household Member". I have noticed that if I use grandchildren, sometimes the connection can be established with the second parent by adding them as grandparent to the child's relationships, but it isn't reliable.
I don't know if this is the same issue or a separate one, but I also cannot have same sex couples adopt each other's kids- if I do it, the next time I go into CAS to edit an outfit, the same sex couple become siblings and can no longer interact romantically. Their relationship panel will read "Spouse, Sister, Soulmate" plus whatever else might make their relationship even weirder.
I can see that this isn't getting a ton of votes, but it is the type of flaw that feels really rough on a personal level- so I hope it lands somewhere on the radar.