In a new database, whether or not the foreign key checks the existing data (WITH CHECK) should be irrelevant because there is not yet any data to check, so the ecript should not fail during the schema creation phase -- the data option to disable the foreign keys should then kick in and disable the dey during the synchronization and turn it back on at the end without checking the data. However, a database upgrade package is a different animal. If the existing data is inconsistent and you apply a foreign key by altering the inconsistent table, then this is something that may need a manual workaround.
If you have got a solid solution to the problem in place, though, I'm glad about that! If you need anything else , please don't hesitate to contact us.