The trick I have is that I add the game and all related windows exes to steam in the same file system. When you run a game on proton through steam, it makes this virtual file system thats matches a game appid, or a uuid. So youll get a folder somewhere thats like 12345566778. You can add that file to an override for a different application, and have it run on that application file system. So if you add a patcher, mod tool etc, you can use it just like its in windows.

For example: Add Diablo 2 exe to Steam. Run Diablo 2 in proton. This creates a folder like 123455 /home/user/.local/share/Steam/steamapps/compatdata/123455/. Then Add LOD to Steam, add this to the system launch STEAM_COMPAT_DATA_PATH=/home/user/.local/share/Steam/steamapps/compatdata/123455/ and you can run the installer on the older file data. Do the same for a mod patcher, etc.