Another roof question - best thing to strap items down with?

Why are you wanting to strap the bikes on their sides? Your truck is not that tall. Set them up just like they were on top of a SUV, with a bike track. Take a bar and run it between your crossbars,perpendicular, and bolt it to the crossbars. They just mount the track to the bar and set the wheels in their on wheel holder. Bike teams do this all the time.