I have the same rack and do the following:
1/ zip tie some 25mm pipe lagging around the offending pedal
2/ turn the handle bars round on the inside bike
3/ with both bikes on the rack strap the crank arms together so that they can't move
Bit of a faff but no scratches or dents yet, and that includes some really bad roads and farm tracks.
The pipe lagging isn't really needed but it gives me some peace of mind when positioning the bikes