Is there a non-DDL way to preserve back-references when staging data into production?
I would suggest adding a (set of) staging tables to the destination or an intermediary that can be better controlled and more stable. Place the tracking info there. Then do all the transformation from the staging to the final destination, either carrying the tracking info with it or discarding it.

There are several ways you can generate a tracking key from multiple systems, as long as they all follow the same algorithm, it doesn't have to be an INT. It could be a 2 char prefix with a sequential number. For that matter it doesn't have to be just one column.