I have a Leer fiberglass cap with thule racks on top for the kayaks. The bikes and lots of other bulky stuff go under the cap.
The cap doesn't cause any scratches. Sits on the plastic rails with foam in between and is clamped down inside.
Recently lifted the cap off with a homemade pulley system and overhanging tree branch to get a load of gravel. Doable, but I don't need to do it regularly which is good.
Next time I'm going with one of those construction style Aluminum caps. They're lighter, and as shown, can come with side doors and inside tool boxes. The Century brand also comes standard with a rack on top for ladders, or canoes and kayaks. And, yes, I would get white to reduce the heat inside some.