what I'm concerned about is being able to flip the extender back into the bed when not in use. How close does the extender come to the tonneau cover rails when you are flipping the extender back and forth? My rails stick out probably 1.5 - 2" further than what yours would because of the wings that activate the track. What surface of the bed sides does the extender actually mount to?There's at least 3" clearance at the rear of the bed between the top of extender cage and the hard tonneau cover rails. I have a BakFlip MX4 and the top of the panel sits almost flush w/ the top of the bed rails. The two plastic vertical uprights at the center of the cage sit at least 2" below the bottom of tonneau panel when the cage is rotated forward.
You should be fine. I have pics but Photobucket isn't plating nice right now.