If a database connection contains users, attempting to enable Automatic Migration and connect to an external database, it returns the following error in the Dashboard:
Error! This database contains users. You cannot change “options.enabledDatabaseCustomization” setting.
Using Automatic Migration to migrate users from an external database into a regular database that has users is not supported.
The alternatives for this use case would be to import the users through Bulk User Import, or to use a second database connection to import the users through automatic migration.