The rack is not metal to metal on the attachment to the car. The clips that go into the door openings have a piece of vinyl tape that helps protect it. Under the towers, those white pads, are rubber. When you tighten down the straps it helps the rack set down nicely without damaging the roof.
If you tighten it down nice and evenly you don't have to worry about them moving. I've driven a good 2,000 miles with this thing on now and it hasn't moved a single bit.
The removal is so easy I wouldn't bother drilling holes in my roof. IMO that's asking for trouble.