Wait, why not? I've been doing this for a few games so I can play on Linux or boot to Windows and play there if I need more reliable remote play or better performance. I haven't had any major issues, just annoying occasional proton reinstallation when I'm in Linux.
@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
I didn't know that I wasn't meant to run windows game off ntfs, didn't have any issues but the drive did die recently (bad sector) I'm assuming this might have been the reason?
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.