Hey Fourfa,
Here are some of my thoughts.
A 4" flat step up would seem to be an aerodynamic problem as I would think this would cause a laminar flow separation along the entire length of your cap as well as a fair amount of turbulence. Which is why I’m too sure, being the smarter than average bear that you are,
you have created this post.
I can't think of any way to put something on which is in contact with your cab that wouldn't destroy the finish. Maybe you could adhere a thin piece of metal at the contact point to act as a sacrificial wear plate.
You could fabricate a solid "AeroVisor" to attach to the top front of your cap which extends forward 6 inches or so over the back of your cab and is held 1/2 - 3/4" from the surface of the cab, it would reduce the aerodynamic upset, and not being in direct contact with you paint, would be relatively trouble free.
Either way, you are right to be concerned, the bed of your truck moves a surprising amount in relation to the cab, even during daily road use, not to mention boon dogging.
I’m certain others in this forum will chime in as well with good ideas.
Good Luck.
Charlie