I have a Snugtop canopy on mine, ordered it new. That canopy is fiberglass construction and has sides that come down over the bed rails. No, there are no paint scratches, but the plastic bed rails have been slightly scratched from taking the canopy off and on.
The reason I take my canopy off is so once or twice a year, I put my ATV in the truck bed and haul the TT. I will tell you, that canopy is very heavy. Two strong men can remove it but it is much easier for 3 strong men to put it back on. You also do not want to lay it on the ground so I built a wood frame it rests on in my 3rd garage bay.