Ahhh. Mea culpa, I am one of those Windoze lusers. Hopefully another Linux guru can give you a hand with that.
All I can add is that my steam version is .723.1 and I took the install files for .725 and overwrote the steam files with them and the game ran just fine for me (launched the game from within Steam), it even showed it was version .725. When I ran the integrity check on the files it reverted it back to .723.
So, unless Steam Proton does something crazy, you should be okay to overwrite the files as long as you don't try to verify the files through Steam.
Unless someone can answer your question, YOLO it. If it fails, you should be able to restore the steam version by just verying the files again.