Congrats on the new truck. I did the same thing. While getting ready to buy a silver at4 the truck came in and brought 4 new ones. One was a carbon pro with 6.2 in black. I had to buy it. I have modified a backflip cover once to work with a ladder rack on my tundra. I think it would not be a issue but I spoke with the people at backflip and they are working on one.if not out by October I will modify and post what I did. They made one for the Honda Ridgeline that has no rail also. Works with screw locks.
Did you get the kicker system in the tailgate?