I too have found that you can have multiple boards within one project and have had success with it but find that the size and controlling access by multiple users the be the biggest hurdle (let alone automating the partslist process). I've abandoned this approach because copying schematic data from project to project (circuits, sheets, blocks, etc) is easy enough already.
We use a Project Template for new designs, not to be confused with the separated ones Mentor provides (new schematic project and PCB layout template). Creating a new schematic project in Dx does not provide a CES database, a CDB nor a PCB. The same, as you know, is true for creating a new PCB; there must be an existing project. The Project Template that we use is really a very small (complete) design. It has one discrete component, two nets, a CES database with a few Net Classes and a synchronized PCB database. Users click "New Project" from Dashboard and the project template is placed in their account. They then rename it something sensible and they're off.
I have had to write code that will rename the project file, the pcb file, the directory where they live and update all the references so that the user gets no error messages when opening the newly renamed project. This was done for the Unix environment users and is relatively simple using perl or bash.