Just consider the scratches part of the breaking in process for the car.
I'd don't think there's any win-win situations in hauling bikes on cars. I have a trunk mount rack, and I've surrendered to the god of scratch. I've been as careful as possible, but the straps and hooks have scratched the surface, pedals have gouged the bumper, etc.
FWIW, I've had success wrapping old tubes around straps that I use to secure a kayak, and that seems to have eliminated some scratches. Maybe some rubber between the foot of the rack and the car?
I've also had bad luck with road debris kicked up and dinging bikes. I've dented a frame and a rim due to road debris. I've thought of roof mounted racks, but I park in a garage, and I've heard too many stories of people forgetting the bike is up there.
Best solution is to go car-free!
