Just to follow up and admit I’m a dumbass. I didn’t look closely at how the Retrax rails slid into the OEM ones and completely missed the upper channel fitment. As you can see from the picture, the Retrax rail was just sitting on top of the OEM rail. I assumed that if the Retrax clamp fit into the OEM rails, all was good. On closer inspection, it was obviously wrong.
I still don’t like the interference with the RamBox, Retrax’s response was “well it did that on the older model too, feel free to trim it”. And like others, the tailgate seal is just barely touching the tailgate and won’t seal anything.
Still, it’s way better than the POS I thought I was stuck with. Thanks all!