In the 13 years I had a CR-V with a hanging rack on the rear, I drove something like 40K miles with aluminum and CF frames on a hanging rack. This included many trips back and forth across the US. Zero issues, and you would be hard pressed to tell where any of the bikes contacted the cradles. The only scratches I got were from where I made a cradle repair using a hose clamp one time and I scratched a frame getting it on and off the rack.

I would make sure to run a strap through the wheels to keep the bikes from swinging on the racks.