John,
You definitely do need Note 2242290 in your system for the sync data to look correct. This does solve the problem with the payroll simulations giving those warnings, too.
Then, when you run the sync in DEV and create transports, even if there is nothing in the TUB level to sync, it will update the data about the Cyclic and TUB in the "sync" tables and put those into the transports. So, it isn't necessary to re-run the sync in QAS or PRD just to update the reporting in the sync tool or payroll log; just import the "sync" transport.
Cheers,
Matt