Finally had the dealer take a better look at it today. I didn't want to pull up any of the trim or the door gasket to ensure they couldn't blame it on me doing anything.
So, we popped up the plastic door sill... Perfect condition.
pulled up some of the door seal, and perfect along the pinch weld. The rust is coming from the ends of the gasket where there is a little piece of metal on the inside of the gasket, likely designed to give it some rigidity to stay put. Since the gasket isn't solid, that is where the gap is and where the moisture made contact with uncoated metal. It's pretty heavily rusted, but since it's right where the water was draining through in this constantly wet weather, it was making it look way worse than what was really going on.
Still, the dealer hadn't seen anything like it before, and neither have any of my buddies with the same body style trucks so it must be rare.
Dealer is replacing all 4 door seals and it should be good to go!