I just had a Leer 100XQ installed on my 2014 RAM. They left the plastic bed rail caps on, which makes sense to me because I like the possibility of removing the cap in the future. Note that they did replace the tailgate cap with one that seals better.
Cap is fairly well built, but I the install work was not up to quality I would have liked. Pics below show truck with cap and a detail of the back corner where you can see the plastic bed rail still in place. Note the overspray on the liner from the factory.
Coincidentally, I am in Dayton, Ohio. I installed the cap for English Springer Spaniel transport to far off hunting locations.