The "all files permission" does not let apps access the private/internal data of other apps unless you have a rooted phone. This is Android by design.
No app in your device can read Joplin database/datafiles. You can navigate to the folder from your explorer but the content can't be accessed.
When you export the database as a JEX container, it will be placed in a global scope folder (example downloads) and other apps can access it if they have the "all files" permission.
This type of data isolation is also implemented in iOS, MacOS and Windows Apps ecosystem (not Windows native).