Cryptomator is designed for storing encrypted files online via (a slow) internet connection. It’s purpose is not to work as encrypted partition where software is running in.
I guess this is why there are often problems when people try to run software direct from the vault.
This is just not cryptomator was created for.
I recommend veracrypt if you want to encrypt local used partitions.
https://community.cryptomator.org/search?context=topic&context_id=746&q=Veracrypt&skip_context=true