"Was the estimate in writing? If so, they are liable to stick with that estimate"
After working in Collision Centers for 40+ years, the estimate you received is exactly that! an estimate of repairs. But, the two tone paint should have been caught on the original estimate, that IS the estimators fault. The upper bed mldg, it's a 50-50 chance of breaking. i always figured one, then if it did not break, i would take that off.
Chrysler sells the bedside 2 ways, with the inner or complete, or without the inner a skin. which one did they figure? and which one was used? ask to see the old bedside and take a couple pictures of it. There IS a big price difference between the two.
I know in the shop I just retired from, if there was a customer pay vs insurance, and something was missed on the estimate, we would always let the customer know, and a lot of the times would work with them on the cost. Parts prices, we have no control over, and the estimating systems are at least 30 days behind the manufacturers on price changes.
Good advice ask to see the invoice, you don't care about their cost, (get the part number off the invoice) ask to see the old bedside, see if the inner & outer were replaced., Call the dealer with last 8 of the vin, ask for the retail on the complete bedside, and for the price of the skin.
Hopefully you have photos of the damage? Another thought, if you have photos, call your insurance carrier, ask them to have their appraiser review the estimate, and see what they come up with. Your insurance company has a contract with you for the repairs to your truck.
Another thought, once you see the invoice, better yet get a copy, call the dealer parts, tell them you are an appraiser for xyz insurance, and need a copy of the invoice, and the "return' invoice. There ARE shops out there that will send back a complete assy, and re order a skin, then bill you for the complete. It happens a LOT more than you would think!
Other than that, get all your ducks in a row and take them to court. Before you leave the shop, inspect the vehicle over complete! and get a written copy of their warranty. Most shops offer a lifetime, but get it in writing.