I'm also interested in perhaps the creation of a program ... that would handle all the changes
Given that you're already using Steam with Proton, this sounds like it might fit the bill: https://github.com/simons-public/protonfixes
It would also allow you to contribute any fixes you've already made so others can benefit from them too; more here: Writing ...
First prepare a new wineprefix properly:
# lets say WINEPREFIX="$HOME/CoolGame"
# Inside the WINEPREFIX for some specific game, I created a new folder like:
ln -s "$HOME/CoolGame/drive_c" "$HOME/CoolGame/_NewInstance_/drive_c"
cp "$HOME/CoolGame/"*.reg "$HOME/...