Where are they stored right now? In other modern IDEs with the folder-as-a-project concept, they're usually somewhere in that folder (either at the root or in a subfolder), since a VCS/repo base is often expected to be at the project folder level, too - inside that project folder, not its parent. So if they're outside right now, I think that change would make sense, especially as just an option people can use if they want.
It can be anywhere you wish - the "base path" inside the project file defines the actual project directory. From my previous attempts to do something about projects I learned there are passionate lovers of this feature so it has to stay as an option.