Current:
Whenever you select "Preserve group membership" when creating a Plan, JCMA will migrate users and add them to their respective groups, UNLESS those groups are externally managed.
JCMA respects the source of truth of the groups.

Future:
JCMA should have an option/logic to bypass that rule and add users to external groups.
This would greatly benefit customers who use this scenario to manage their users, as it would avoid the extra effort of manually updating the membership before or after migration.

Of course, there might be a reason for that, but an alternative would be very welcome.