the issue probably is that you had the proton/wineprefixes on ntfs which will not work

I symlinked the game folders from a NTFS drive to steamapps/common/ on my ext4 drive, and it works fine. Of course the compatdata and shader caches are on the ext4 drive.

I run overwatch and rdr2 from ntfs partition with no problems. I just created a symlink from the default install path.

@MyFairJulia wait, you can run games from ntfs drives with linux? what ntfs driver is recommended for that? is ntfs3g broken? I'm asking because each time I try to do something like that, I do get permission issues, as you say. Worse, each time windows would make a file, the linux side would come up with a permission error when trying to access it. That's why, I don't use ntfs stuff anymore at all