RamBox equipped trucks do not have the braces at the front of the bed because the thickness that the RamBox bedsides provide enough support for the dual-function tailgate.
All non RamBox equipped trucks with the dual-function tailgate will have the two braces at the front of the bed for extra structural support for the bedsides when the dual-function tailgate is open. So do not remove them.
The Mopar factory tonneau will work on both beds with no problems, the clamps on those tonneaus wont interfere with the braces, the only issue I see the braces having on the non RamBox equipped trucks is on the aftermarket tops/tonneaus may have mounting point requirements in the general area the support braces are sitting.
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.