When you say cover are you talking cap or like a roll up tonneau cover? Truck rack meaning ladder rack? I have a ladder rack for my truck that fits around the cap, but I am not sure that is what you are looking for.
The holes in the bed rail are the retangle shaped stake holders that a ladder rack or a full sized work rack, where you can load ladders, plywood, etc. will set into. I would like to find a cover that I can still use these stake holders and the cover at the same time. I looks like most of them cover up at least some of the hole, which makes them useless.
I'm not looking for one of the fiberglass lids, we need to open the bed up too many times and carry things that just wouldn't fit without taking off the lid. I would prefer a roll up type system such as a Roll N Lock or a Retrax but will go to a tonneau cover such as a Truxedo if it fit the bill.
Does that help or is this description still too vague?
The link is the guy that made my ladder rack. It fits around my cap and is bolted to the truck. I can remove the cap without taking the ladder rack off of the truck. I don't see why it would not work. He custom makes them to fit your needs. His work is top notch and he is not that far from you. He made mine and shipped it to WI. If you click on my avatar, I have more pictures of my truck with the rack so you can see how he made it.