GE-Proton (proton-ge-custom on github) depends on and is built for use only in Steam, alongside Valve’s official Proton releases. When installed, it shows up in Steam’s “compatibility tool” list.
Wine-GE-Proton (wine-ge-custom on github) is a custom version of Wine with some hand-picked patches from Proton’s source code, built to run without Steam, either standalone or with game launchers like Lutris.
Yes, GloriousEggroll is terrible at naming. But he’s doing a good job with functionality, so getting used to his confusing names is worthwhile if you have a need for this stuff. :)