Rust is a very illusive problem, the bed liner sprayed on the bottoms of the doors sounds good, but the problem is rust don't start on the out side where you can see it. Instead, it starts from with-in, down in the cracks and crevasses of the doors, fenders and wheel wells. Number one reason for rust is the built in drains get clogged up and don't allow the water to escape. This trapped water is even worse in winter months, then it becomes trapped salt water. Also, I do not believe Dodge treated all the inner doors the same, I have seen some with a coating and other without? I recently checked my and it was coated and the drains were free, consequently the door was in great shape. It is important to clean the bottom of the doors each time you wash the truck, this area gets alot of build up from the road grim splashed up by the front tires. I suppose this is also what clots the drains? I always go over the doors and their sills, wiping off the grim and looking for any trouble signs, it only takes a few minuets.
Also, any time you add an accessory like wheel well trim, mud flaps, bed accessories or anything body mounted, make sure you use some sealant on the screw threads before final assembly, this coats the freshly drilled whole and seals it against moisture entering at a later date. This is especially true when the areas are on the sides or under the truck, I have seen many trucks that have rust spots that started in areas where something had been attached. Most everyone adds something to their trucks, that is what makes them "Their" truck, just think about it next time you have to drill some mounting. Items like Nerf Bars and running boards are the worst, they live in a high risk environment and if not installed with caution, will be a source of a future rust spot. I think running boards do more harm then good, they require many fasteners to secure them and they fit up tight to the lower body panels. This gives salt,grim and everything else a great place to hang out, by getting trapped between the boards and the body. I have seen many trucks and vans equipped with running boards rusted out in that area, the worst spots seem to be where the front supports attach, which makes séance that is where the front wheel throw the water. Some guys are lucky enough to live where salt is only used as a food spice, but for the other, myself included, extra care has to be taken. I had the popular wheel trims on my truck, the ones made of SS and go over the wheel arches. If you have these or are thinking of adding them, please be very carefully these have two problems. One, they attach to the inner side of the wheel opening, these is a very bad spot to drill and attach something, it is constantly being spa shed with something. Two, the SS wheel trim pieces have a rubber lip that goes around the outer side, it separates the trim from the body of the truck. This rubber breaks down in a year or so and ends up scratching the trucks finish. Also it allows grim and Debra to be trapped between the trucks body and the trim piece, resulting in a perfect place to start rust. By adding these pieces you will also void Dodge from any responsibility of the effected areas, bottom line is you will have to pay to get it fixed. Accessories are nice and everyone likes them just think.