I'm not sure what kind of back rivet set you are using, I used one of these:
http://www.cleavelandtoolstore.com/p...p?number=RSB35
I primered my parts before riveting and had no issues with the back riveting set marring the stiffeners. The collar that contacts the stiffener is plastic. The actual rivet set is steel but this should only contact the rivet being driven. I strongly recommend riveter's tape on the manufactured head, both to keep the rivets in place during back riveting, and also to prevent scuffing the alclad when driving the normal way. When I finished the back riveting, I dipped a Q-tip in primer and placed a drop on the shop heads.