I tried to mod Cyberpunk 2077 and it was not a smooth experience. I first tried using Vortex in Bottles but it wouldn't run. I then tried to use ProtonUp-QT but couldn't figure out exactly what to do. I discovered that there's a new NNM AppImage that's early in development that works with Cyberpunk.
I'll have to try again in the future and figure out how ProtonUp-QT, ProtonTricks, Steam Tinker Launcher, etc.
Vortex absolutely works in Bottles, I use it myself to install and update the Welcome to Night City collection.
try the following guide and adapt it to Bottles. if you’re using flatpaks, you’re likely facing the permissions issues that are mentioned in the guide.