So that every time you open a project it looks just within it's directory for assets. This way I could have a folder and within that folder I have generic named assets that when I open the after effects file in that directory, it reloads with what's in it's local directory. If anyone has ever used 3DS Max, it would be similar to how their project folder system works.
Personally I think the folder structure set up that you get when you use the collect files feature on a project is about as efficient as it's going to get. Project goes into his own folder and then subfolders are created for the assets.
This may be a good item for a feature request.