Just gonna chime it with my two cents.
First off... It's RUST. You guys both live in areas prone to rust and corrosion due to the chemicals and minerals they put on the roads in the winter to melt ice and snow. I know, I lived in the east the bulk of my adult life.
"Discoloration" in paint should NEVER happen. If it does, this means the paint isn't sealed with the clear coat and needs to be repaired under the vehicles exterior paint warranty. Road grime washes off and is NEVER reddish unless you live in a trailer park on Mars. NOTHING should EVER penetrate a Urethane finish (which your Jeeps both have).
The reason it's rusting is that Chrysler in it's infinite wisdom implemented cost cutting measures (to charge more for less) and has removed certain steps in assembly of these vehicles. In the past, parts were painted, then installed. Your Jeeps are assembled then painted, leaving unprotected, bare parts under mounting areas.
DO NOT let the dealer jerk you around... It's rust, pure and simple and needs to be repaired and IS covered under the "paint, rust and corrosion" part of your warranty.
That rust isn't going to start creating holes until AFTER your warranty runs out. This is why they tell you it's road grime. And by then, it will be too late and you'll end up replacing the windshield frame and have to have parts of the tub cut out and welded back in.