Kuroko: And more and more and more... some of the most notable non-gameplay things that people should be aware is that enhanced edition has a different EULA to the regular Quake which prohibits e.g. modding basically.
I don't know what the EULA says, but it's not legally possible for an EULA to obstruct your ownership rights over a piece of software you've bought and owned, which includes the right to modify it as you wish.
What you can't do is then distribute your modified copy of your game, because you don't have a right to distribute the IP. But you can distribute the files to modify a copy of the game so that other people can also modify their copies of the game.
And you don't have a right to use a modified copy of the game on servers owned by somebody else, such as Bethesda. They own their servers and can set the terms for your use of them. However, they cannot reach into what you do with your offline copy of the game.
No matter what an EULA might say, people are lawfully entitled to modify their games.