Yeah, that was total BS. Warranty is warranty no matter what dealer sold the truck or what dealer services the warranty.
Hand him a cold Snapple on a hot day and tell him thanks for the help. Your visits will go better.
In fact, here's a tip to improve your relationship with the service department. It's called bribery
One morning, early into their shift, take a box or two of donuts to the service department. Make sure you have enough for all the service writers and techs.
On a hot afternoon, take in a cooler full of ice cold Snapples or other non-alcoholic beverages.
They will remember that. And they will be more attentive to your needs.
One caution - don't do anything that the service writer will do without them knowing it, like ordering your own parts under a warranty claim. Let them do their jobs.
As far as the bed caps, I never liked them. They all did the same thing as yours. One of these days, do a spray lining with a "topper edge". Thats' where they line the bed and the top of the bed rails.
Looks good, won't warp, lasts forever.