I don't have the molle panels, but I do have the tonneau cover. Just taking a guess, but could the issue be because the tonneau requires lowering the factory rail?
Doesn’t seem to line up but I’m told by dealer that it works and they can do it. I asked if there was a part needed and they seemed to play stupid.
I have the bakflip MX4, which basically mirrors the OEM install. The rails don't have to be lowered on the bakflip MX4 and I'm mostly sure that the OEM doesn't need to lower the rails either, but I could be wrong. That being said, it is a tight squeeze once you try to get the hardware in there to get the molle panels to fit properly. I had the Trumgeta version and it took some effort. At points I had to unhook the tonneau cover clips to slide in the nuts into the rail.