Yes, I'm aware of the size of difference,
Some caps can accommodate this with a flat bottom (where cap meets bed rail) that is a few inches wide. On one truck it will fit perfectly, on another,it will hang over or show the bed rails a little. Just depends on how it is made. And of course, a good seal needs be made with a rubber gasket/bulb seal. I ask because some caps work, like AT Overland, they designed it to work, and some don't, like LEER, they have an apron that comes down over the outside.