For those who don’t know, Proton is the tool that the deck uses to run windows games on Linux. GE-proton is an alternative build of proton that includes extra fixes for games, media codecs to fix video playback, and more. You can easily install GE-Proton by going to the discover store in desktop mode, installing ProtonUp-qt, and then selecting GE-proton from there.
The way that GE-proton is improving mod support here is by recognizing common mod launcher .exe files such as skse_loader.exe. If it sees a mod launcher executable in the game folder it will use that instead of the original game launcher.
If you install ge proton, on steam when you open compatibly options you can choose any version of ge you have installed. I use it all the time. I use proton up qt from the discovery store to manage ge proton versions.