Once protected, backups at instance level should work seamlessly even if a new DB is created. This does not require any manual operation/update (other than resource discovery) on the SnapCenter side. The consecutive backup operation should automatically include the new DB. Isn't that working?
Yes, since the protection is at instance level - exclusion of individual DB is not possible. Even if a DB is not in the proper state, the backup job should be giving a warning against that particular DB.