Platform Designer and DSP Builder

You really only want to do something like that if the PD system will be the top-level design entity for your project. And of course, if you have other .qsys files for other systems in the design, they need unique names.

.qpf is your main project file and its name gets set when you create the project, usually with the New Project Wizard. You can set the top-level entity name in the New Project Wizard as well (so it can be unique from the project name) or change it later.