I have an Impreza with a similar flat roof. I purchased a Yakima system @ Gi Joes because there was a hefty going out of business discount. The system has feet (towers) with a 1/4" or so dense rubber pad. Wide hooks then grab the metal edge of your door frame. I have zero damage on my roof due to the racks. Having said that, I have heard that some of the newer cars have plastic surrounding the door frames. This may not be an ideal clamping surface. Call Yakima or Thule customer support and discuss your particular vehicle. I also have a sunroof and it is able to open & close with the rack installed (check on your vehicle though!).
I have the Yakima High Roller bike rack and it is very nice (no need to remove tires, etc.).
Oh yes: When you order your system, the company will specify a certain length crossbar. Longer crossbars can be used for more roof-top storage but you run the risk of hitting your head each time you enter/exit the vehicle.