You can have it one way or the other - either the metacourse synchronizes a role from the child course, or it doesn't. Which roles are synchronized is controlled on the user policies page: Site Administration -> Users -> Permissions -> User policies.
You could maybe do something like have 2 separate student roles, one that is synchronized and one that comes from your external enrollment database.
Roles and permissions
Metacourses - Possible to have enrollments directly into the Parent?
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