Brian, thank you for this very detailed explanation.
I would like to add that currently there is a bug with Project Server 2013 that blocks Project Site Permissions synchronization alltogether. After installation of September 2014 CU for Project Server and SharePoint Server, the Project Site Permissions sync
fails. Queue jobs are created but the job 'Prepare Project Web App Permission Synchronization For Projects' fails for all existing Project Sites, due to a change in behavior in the September 2014 CU.
Microsoft is aware of this issue, but no date has been communicated when it will be fixed.