Imagine you work for a large company that uses Microsoft Project Server. Since you have many employees, having MSP sync individual permissions for every user to every site is simply not scalable. Instead, you’d like to use some Active Directory groups that are already set up to manage permissions in the workspace.
So you disable the workspace permissions sync in PWA:
Then, perhaps you write some code that is wrapped up in a nice SharePoint feature to manage setting up the permissions yourself. Everything works great….
… until you start getting reports that some user’s permissions aren’t quite right for some project sites.