The workaround I've come up with for the T5UTD issue is to not use the client-specific transport. The sync tool itself seems to work just fine, it's entering the data into a transport and then using the transport that causes the problem. Specifically, it seems to have a problem with deleting rows with an end date of 12/31/9999.
So, for now, my procedure is to use the cross-client transport, but to manually sync client-specific data for the downstream systems. This, after painstakingly fixing erroneous entries in my first test system...