If all content versions are not visible, then you need to make the below additional settings:
- Go to Setup and search for Permission Sets (choose an existing one or create a new one).
- Click on the App Permission, then Content.
- Select the "Query All Files" option.
- Assign the newly created permission set to the user who has a Mass File Download license.
Note: Query All Files is not enabled by default for the admin user, but you can at least enable it in a profile/permissions set.