See: Matrilineal Marriages, Gender Equality, Same-Sex Relations, and Sexuality Distribution
"The core engine" doesn't do what you think it does. It's actually a running joke on /r/paradoxplaza that every time you mention Clausewitz, Meneth (or one of the other developers) pops up to explain this. It just does what every other game engine does, none of the actual game mechanics are coded into the engine. The reason why all Paradox games have so many things in common—a map-based UI, the scripting language, everything else that makes a GSG a GSG—is that game code gets copied and pasted from game to game as they start new projects. None of this is in the Clausewitz engine itself.
Funny thing though, they actually did decide (relatively) recently to centralize a lot of basic GSG functionality in one place so they don't have to keep copying-and-pasting code. The result is a library called Jomini. But this is a recent development; the only games so far that use Jomini are Imperator and CK3. It's a very new library, so it shouldn't have 15 years of legacy cruft in it.
If they made it by copy-pasting one last time, it certainly could.
If you make it equal, you remove the drama. If you force equality onto history, you falsify it.
Case in point: Edward II, king of England. He had affairs with Gaveston and Despenser the Younger, all the while in a marriage with queen Isabella. He wasn't too subtle about what he was doing, showered his lovers with gifts, prestige and land. His nobles pressured him send him away, but he was the KING, and it went back and forth a few times.
If it's in game, it should be called "sodomy".
imho the thing to do is take OPs suggestion, Paradox should make gay-marriage possible but have people refer to it in variable ways. Some egalitarian societies can call it marriage, others sodomy, etc. And then add other cross-cultural restrictions too, where civilizations may not recognize bi-religious or bi-racial marriages for various reasons.
In other words don't minimize the issue, lean into it in a CK way, deeply and unsettlingly.