Or you just buy these black plastic plugs for it. Same things the Chevy crowd has had to use for years. You might see if a shop will colormatch them for you, then it won't be so noticeable. The bolt holes are down so far, I don't think a tailgate cap will cover them up. But I may be wrong.
Look at the first post in this thread. Dave posted pictures of his truck with his new tonneau cover on. The tailgate spoiler is removed and the plug caps in the holes. Thats an awful long ways down from the top of the tailgate for a cap to cover the holes. Not saying none are out there tall enough, but its gotta be a tall ass gate cap.