Galaxy is just for automating installation and updates and implementing cloud saves and achievements. The installation is identical to one made with standalone installer and can be launched from the executable without running Galaxy client. Already installed games can be imported to Galaxy library.

Proton is kinda tied to Steam, but UMU already replicates those dependencies so you can run it outside Steam client, so GOG could do something similar and I doubt Valve would object cooperation if GOG wants to participate developing Proton.