Or they did notice, figured out it would be complex to modify the engine to handle this case, found data indicating that having this feature or not would have zero impact of the marketability/sales of the game, and just decided to use the bandwidth on something more valuable.
It's a one-byte modification if you want just to remove the check for mixed genders upon marriage. If you want to implement as proper game feature - as a selectable option - then you need to do a bunch more things; you need to model the conditions in which that same-sex marriage would be permitted (even if it'd be enabled in the game as such, there would be character-faith-related conditions), you need to model how every other character would treat that marriage (a bunch of conditional modifiers depending on the attributes of that other character), you need to decide how it interacts with polygamy if someone has spouses of both genders; you need to adjust for any impacts on the many inheritance models (after all, the main gameplay purpose of marriage as opposed to just lovers is the effect on inheritance); you need to adjust any events and event text (and translations) where it does not make sense any more; you'd likely need to change the treatment of bastards if one is born in a woman-woman marriage and you need to treat edge cases such as regency if both spouses are pregnant (from other partners) at the same time; etc, etc.
CK3 has a lot of modifiers - you can simply have this as one of them.
You don't need to do any of the above, everything else you mentioned is something that can be done in the scripting language. The community will do it for you. You just have to hide a toggle somewhere.
Maybe adding same-sex marriage just isn't important for game from times where same-sex marriage was non-existent. I want rocket jumps in every game but I doubt my desire will be fulfilled.
The author acknowledges themselves: "The patch that I made was only good for the current Steam version of CK3, on my operating system, with my cpu architecture."
Not counting the fact that a change like that would need to be more thoroughly QA-ed to make sure it doesn't break something at some point.
Yes, of course. That's the cost of same-sex marriage in such a game, unless you use the House Seniority mechanic you will eventually have a game over. That doesn't make this anymore difficult than switching a false to a true in an optional fun feature, it'll just be very difficult to play the game (but not impossible!)
Elective succession and tanistry were rather common historically and an option in the game, so having kids shouldn't be significant. The key is the heir has to be in your dynasty, not that it be the fruit of your loins.