using a modding API is a lot easier than forking an entire source tree and building the application yourself
Why is that ease worth it?
also, a lot of modding APIs present a cleaner interface than directly editing the source would.
How do they do that?
also i read the page about forking and it seems to have little relevance here. it focuses entirely on tools, that is, software which performs work. games are entirely different, because they are intended to entertain.
I really don't like the mentality that video games are somehow special pieces of software. While it's true that the purpose of video games is to entertain, that doesn't mean that a video game can completely ignore the fundamental principles of software design (i've talked about this before as a part of this thing). The idea behind the page that "a fork of copylefted software cannot survive unless it fills a niche unique from the original software" is, i think, completely applicable to video games.
folding every mod anyone has ever made back into the main branch and putting under a menu option would be hopelessly impractical to manage and it would push source tree and binary sizes through the roof, for features that a lot of players won't even use.
Exactly, which is why i don't advocate for that. Only the mods that are good and are competing in the niche that the original software fills should be merged into the original software; mods that compete in other niches could be merged into forks if they happen to be good.