If I were you I think I'd stand the whole thing on a 5 or 10mm thick rubber pad the size of the foot print with additional rubber buffers either side made of the same stuff. Look online as you can order rubber matting off the roll. The crate box won't damage the floor rails with a rubber buffer underneath and it shouldn't move at all forward, aft or sideways. As it is it may slide on the alluminium floor rails when under heavy braking. To stop it moving forward perhaps you could have someone make up a heavy duty aluminium angle with a security fixing to each of the floor rails. I can see a ratchet strap getting in the way and proving annoying.
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This photo shows the front end of my Calicap boot tray. It is held in place by four twist fixings the same as those used on the Multiflex board. There should be a VW part number so it should be possible to order four. So if you had a heavy duty steel or better still alluminium angle going right accross the van with four fixings to secure it to the foor rails the crate box couldn't move forward. Even better still, bolt the said angle security rail to the forward lower edge of the crate box and it won't move at all. No ratchet straps required.
You must have realised you will have to relocate your jack, removable tow bar etc.