This is a GUESS. Please don't hold me to this.

The factory warranty which many people refer to as a "Bumper to Bumper" isn't. However there is a "Bumper to Bumper" for the 1st 12 months / 12,000 miles. This is where your brakes; wiper blades; clutch discs; windshield and rear window; and wheel alignment and wheel balancing are covered.
These are replacement items that are not covered under the 3yr/36. This was taken directly out of the supplementary Crossfire Warranty Information book that comes with your owners manual.
I have replaced 4-5 pairs of headlight lenses under warranty with no problem through Chrysler. I think your dealer is trying to put your headlights into the items mentioned above.

Not picking a fight, just giving an opinion.