The only changes that we do to the database when you use SyncSvcUtil is to use the SqlSyncScopeProvisioning/SqlSyncScopeDeProvisioning API's from SyncFx 2.1 to provision/deprovision the database based on the request.
This means that we create insert/update/delete triggers, tracking tables and few stored procedures per table for change tracking/enumeration/change application purposes. This is exactly similar to what you would have done, had you used SyncFx 2.1 to manually
provision the database.
SDE, Sync Framework - http://www.giyer.com