the point is quite clear. running multiple incompatible versions of the same program is quite a miserable experience. having your favorite mods not interoperate is an unfortunate experience. as for submitting patches to the main game, this is not applicable for certain mods. many of my favorite video game mods definitely would not ever belong in the main game.
you could ask the very same question for proprietary games. in the case of minecraft, there was once a time when things like forge did not exist, so to make mods, people decompiled the game, made the modifications they wanted to make, and published the modified classes. to play the mods, people could just extract the classes into their minecraft jar. however, much like multiple incompatible forks of the same software, this does not provide good interoperability or a good user experience, so mod loaders and APIs were developed to provide this.