I just confirmed with KP2A the error of EBADF bad file descriptor. I was able to create a test db file on proton drive. But that tells me something. It uses the file picker to create the db file, which doesn't require KP2A to have storage permissions. The File Picker uses the build in file explorer, so it sees the Proton Drive and can read and write to it.
Once the database file is open in KP2A, it probably relies on it's own permissions to use the file, and can't do it.
Storage Scopes doesn't seem to see the Proton Drive either.
My guess is that Proton Drive has an API that the File Picker/Explorer can use to do encryption/decryption on the fly. But other apps cannot. KP2A has a short list of cloud storage apps, Proton Drive is not on that list at this time. No idea if they want to work on that, or if its possible.