If I understand correctly, I agree that it would be nice to allow the client to add specific paths in addition to the server-side settings. It would also be nice if the server would gracefully handle duplicate directories/files.
One of my first test clients was setup first on the client side paths, but I determined it best to use the server’s central admin to set the paths. This client does not follow the server-set paths. I uninstalled the client and re-installed to make it work using the server’s path.
I do use the /optional setting on the server side to pick up the exceptional, additional paths needed by only 5% of my clients. That’s where I think it would be nice to use the server settings to backup the majority of the paths and enter the additional paths on the client, if needed.