Unless something has changed with newer models, should not be a problem. The bedrug
fits under the rails all the way around, so, you should be good. Only issue I can see is how the cover is installed and how close any clamps may be to the inner bed walls.
The bedrug is flexible for install, so, should fit okay, without removing anything.
I have the bedrug on board, and it fits nicely with my ARE cover. Bed caps are on top, so, that is not a problem either. (I do not have bed rail caps with my setup).