Tl;Dr: Proton GE has extra game specific performance and compatibility patches that Proton doesn't target for whatever reason.
Too long but I typed it out so might as well post it anyway: This is how I understand it goes like—
Now, we know Proton: a Valve-maintained fork of the venerable Wine project with many many gaming and game specific patches, made for Steam.
Proton can be used outside of Steam, of course, but it isn't really designed to be, there be quirks. Plus, Valve maintains what goes into Proton, so if anyone really wants to play a certain Windows game that doesn't quite run well enough on Proton and put in the work needed to make the necessary changes, it's probably not getting added to Proton just yet (I frankly don't know how or whether Valve accepts PRs at all). And Wine does not really want game specific patches in the runtime. Wine wants to be as generally compatible as possible.
That's why most Proton variants exist. A certain Glorious Eggroll maintains this one, which has quite a few patches for games that aren't targeted by Proton either at all or well enough, as well as making sure it can run outside of Steam (there are other variants of the patches for vanilla Wine or for use in Lutris as well, I think?)