Shorten the rack tails?
Are you S-line or non-S-line? (different rear spoilers.)
I have the same trays on my car w/ the OEM rack. I moved the front bar up an inch or so from the correct install location. The trays now don't hit the Sline spoiler when you raise the hatch. I couldn't cut the tray either becuase my 29er uses the entire tray...
then you have to move the front mount more forward.
I use to have the thule mount on my 2 door, had to slide the front mount way up front. the fork mount bikes barely fit (that was the one w/o the rail). Ski bindings with all the flex extensions could barely fit between the mounts.