I found that while running the Windows version through Proton and GE-Proton actions that cause a large amount of drops to spawn would cause the framerate to crash to 2-3 fps and it wouldn't improve until restarting the game.

Actions that caused the framerate drop

• destroying a silver vein by fully excavating it then hitting it
• colosseum destruction in fader boss fight

Both these actions caused no issues when running the native version