My guess is the shape of the cap, and maybe even a bit to do with the material (ime pop-off caps are a weaker plastic to allow them to deform around the bottle lip). Screw top plastic bottles have deeper caps than pop-off glass bottle caps.

Thus when stored the inside surface of the pop-off cap has more chance to rub against other surfaces and create plastic dust, and being a weaker plastic it may gouge more easily as well.