I wouldn't pay out of pocket either. If its ANYTHING like Toyota warranties.... One lost wrapper or box (yes the want these back for whatever reason) or paperwork not completed and YOU will eat the cost. Nothing against your shop, but do they know Jeeps warranty procedures? Manufactures will do just about anything to get out of paying for warranty work.
Toyotas has been known to have rusty truck beds for a while. The owner must first seek assistance from the dealership. Many papers and what month / year your car was made and does your vin have a "K" as the fifth and "P" as the ninth digit, then and only then the dealership can start the endless process of calling Toyota, getting approvals to even look at the car and get paid... The dealer then has to apply a special coating or if that wont fix it has to request toyota to replace it. Then it comes out to the body shop, we write an estimate. Many hoops later we get the parts in, and we have to save the old truck box, and the big *** box it comes in, the old tailgate and its box, but we have to send the tailgate emblems back to toyota in the replacement packages. Oh and the old truck box and tailgate must be on hand for inspection for 1 year. At one point we had 9 of these sitting out back. Freaking crazy. The tech has to punch his time card while working on the job. All of this and something as simple as throwing away an emblem package means we eat the entire 4k job. We have a lot of "trundra" emblems laying around....
"so i did a full tune up soup to nutts."