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.
To be fair, this isn’t normal proton doing it. In general GE-proton exists to do things that go against the design philosophy of regular proton or to include licenses libraries that can’t be normally included.
I don’t see any mention of it in the changelog, but I would expect there to be a launch option to disable this functionality as well.