I got my GOG Oblivion running with a mod pack by installing and running Vortex. I ended up using this utility:
https://github.com/pikdum/steam-deck/
It allows you to install Vortex in your game Proton prefix (you have to run it at least once for said prefix to exist). Then, after installing mods through Vortex, you use the 'post-deploy' script to synchronize some files, and your game is ready.
No idea honestly, I have no experience with Fedora and this toolkit seems to be designed for Steam Deck. At this point I'd try looking for an answer in the toolkits source files - it's all essentially a bunch of bash scripts moving files around between Proton prefixes, AFAIK