I had rust and bubbling paint under all 6 of the attachment points for the roof rack and the air deflector. The worst rust was actually under the air deflector.
I sanded to bare metal, ground the nut-serts flush with the sheet metal, treated with POR Metal Prep, then POR-15 putty (so the holes would fill), then covered with about an 1/8" thick layer of spay-on bed liner from a rattle can.
My fuel economy went up by 50% due to the better aerodynamics, my kid's grades improved, I got a promotion at work and everyone thinks I am now taking Viagra!
Seriously, I am glad to have the rust treated and the causes of the rust gone. As has been said a hundred times before, just a poor mounting system.