the advantage of mod apis is that you can have hundreds and thousands of mods, all of which are going to be mostly compatible with each other, and the individual player gets to choose exactly what combination they want. if you merged all these features into the base game (or a relatively smaller number of forks) then you wouldn't have that freedom of choice.
and if you are thinking 'well, that freedom of choice doesn't sound like fun to me' that's fine, but given the popularity of modding across a wide variety of video games, it seems like a lot of people have a different idea of fun to you.