Do you mean rails on top of the tunnel? They are typically fastened with rivets. You can drill out the centers of the rivets and pop them through with a punch. It leaves a nice clean hole that you can patch with what ever you desire.
ZR6000 is right on with the aluminum. The only potential for rust is the patch you put in place.
I've patched with a variety of methods on non structural holes. It doesn't take much, just fill the holes. Good silicone or JB weld is easy.
I just took the rack off and moved it 3 rivet holes back. I just had to drill 3 more holes each side. It gave me more room for by bag and the rack is more useful now. Just filled the 3 hole on each side with new rivets.