I left the rails, and with the TC loaded, no one knows. As you posted, I used 2x4, side to side. I have used foam, made a wood frame with plywood on top, and back to the K.I.S.S. method, simply using 2x4s or 2x6s side to side. It has worked for me since 2004 and over 100,000 miles.
I find the extra height allows more use of the truck bed from the sides, and makes it easier to wash the top of the truck cab.
I have used the rubber horse mats, but they are only about 3/4" thick, which is not enough. I will also say they are pretty heavy, and more difficult to store when not in use.
Wayne