more advice
Obviously you would not want your truck done in a shop that you have had problems with before. Does the local dealer operate a paint shop? Have you seen their work? Ask for references. You will either be happy with the paint job or have a new truck. If you are unhappy with the repaint, DO NOT TAKE IT HOME!!! Nobody wants to do this paint job again, and D-C will not want to repaint it again. Whatever shop does the painting will bear responsibility for the job. D-C will want to have it handled in one of their shops if possible. Don't be afraid to check into other dealerships that do quality work.
The decals and stickers in the jambs are there to stay. It is a federal crime to tamper with them. Experienced painters do not leave tape lines or overspray on the truck. Being black, dirt and sanding marks stand out. Look your truck over really well and look for dirt and nibs in the paint. Hopefully there are very few, as warranty work returns the truck to like condition and not a show perfect job.
As far as measuring the paint, I would expect the dealership to do that to determine what needs to be painted. D-C would be aware of problems at paint factories by now. They would know what steps or problems caused this. They would know what areas were affected. Part of the warranty process is identifying who, what, when, where, why, and how. Often the repair process is delayed a little bit so proper investigations can take place to determine exactly what happened and how to avoid future occurances with a cost-saving solution.
Primer, base color, and clear operations take place at different stages along the assembly lines. Just because one may be thin does not necessarily mean another paint operation is also lacking build. That is why paint measuring would normally be done to determine how extensive the repaint would be.
You may naturally see the primer in the jambs and some inside edges. You would have to look at another truck with correct thickness to determine what should have paint on it. I alway buy a two-tone paint truck because a two-tone truck has two color paint jobs on it. That means twice the protection before rust starts.
When I do warranty paint work involving peelers, I use a spray on stripper to remove the paint layer by layer. Using a sander often leaves waves in your paint, requiring an extra prime and sand operation. Black trucks show all. Whatever paint quality you have visually on the surface now will more than likely be the same quality after a repaint. A good shop would try for the best job possible, and not just do the work to the hours that D-C would pay them. A good job would involve removing mouldings and the like.
Sorry for all the long posts. I have worked both sides of the counter before. I have been an autobody tech for a long time, then been a GM service manager, and then returned to body work because neither GM nor D-C would pay enough to do the manager job. A cool head does prevail. Do not be afraid to ask questions about prodedures or quality. Nobody wants to go through this again. I wish you the best of luck, and hope for the best in the long run.