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.
Not sure where you got this from, but Proton, GE or not, has always been meant to be used within a Steam environment first and foremost.