I respectfully have to disagree with you. I own a RAM with the Dual Function Tailgate, and I bought the Mopar cover. It will not fit unless you remove the brackets in the non Rambox bed. The side rails cannot be mounted flush to the sides with the brackets in place. I know this because my dealership tried. At the very least, the brackets would have to be loosened so the rails could fit behind them, and even then, you'd have to notch out the bed cover rail so the bracket bolts could remain in place. In addition, the knobs used to secure the bed cover line up exactly with the diagonals on the brackets, so no go there.
MAYBE, if the brackets were flipped (so the diagonal was lower) and the bed cover rails notched to accommodate the bracket bolts, then it might work. I've been looking into this for almost a week now, and after an hour on the phone with RAM last week the best input I could get from customer service was, "we're looking into it, and we'll get back to you." As I posted earlier, the Truxedo Sentry might work with the flipped brackets and no notches, but I'd have to test that.