I can't raise the lid, but my tailgate is open. Obviously, I didn't install the bags perfectly last time I put them in.
On the left side, looking forward, the studded rail is even with the back edge of the floor mounted metal portion, with only the plastic rear clip showing. That puts the back edge of the saddlebag about 9 1/4" from the rear valance of the truck, measuring at the center of the rail slot.
The right one is in about 2" further forward, with the entire narrow plastic clip visible.
Seeing as I can open both saddlebag covers with no problem, there is some flexibility in mounting the saddlebags.
I would definitely investigate whether the rails have been installed the wrong way. Try installing one the opposite way to see what happens.