I don't carry delicate items very often, but my Alturas have an inner layer between the contents and the back of the fixings, which seems to do a reasonable job of preventing damage by whatever's going on on the back of the fixings. The Brompton C bag, which I'm most likely to use for this sort of thing, avoids this problem by attaching to the frame with a pocket, rather than screws or rivets. With the Ortliebs, the plastic dome nuts aren't very sharp or hard to begin with - my concern there is that they stick out quite a lot and could concentrate pressure if the bag is very tightly packed - I generally try to pack them so that things with crackable screens, solar cells, etc aren't up against the nuts.
Not sure what a Carradice rivet head is like, but this might be a job for Sugru? I used that to give the nuts on the inside of my trailer box (where the feet and refelectors attach) a soft rounded surface.