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.
I have another brand of tonneau cover and bedside MOLLE panels. Had to unbolt the cover’s hardware inserted in the bed rail to get the panels attached to holes in the bed under the rails. But we didn’t have to lift the tonneau cover off the bed. Two pairs of hands made it easy.
Without seeing pictures from inside your bed/the brackets provided with the molle panel, it's tough to offer advice.
My blind guess is that you'd need to modify the brackets so they're able to meet the molle panel at the necessary height to complete the installation. Or, drill new holes in the molle panel to meet the bracket at it's lower height.
I have a rear panel on my truck and had no issues installing, but I don't have an OEM cover, I too have an MX4.