Project Manager, hard paths for include/lib directories?

Didn't somebody fix the issue of hard coded paths in generated projects already? Or did I just fix that manually in my own project? In any event, I notice that when I build projects using the project manager, all lib/include etc. paths are hard coded right back to the root of the hard drive, rather than the more portable "../../../../../Engine" local paths method.

Is there something I need to switch somewhere to fix it or is this standard behavior?