Proton is just emulation, and it will happily expose the underlying host system to the running game software. In particular the filesystem and some peripheral devices. However, Valve is moving towards sandboxing in Steam. You can already run the whole thing with a flatpak sandbox, and valve themselves are using ostree. With srvio is possible to run the whole thing in a throwaway windows vm while the graphics card is passed through

This is why it was foolish to give a new name to it. It was originally called Wine Is Not an Emulator.