after loading my Adventures on the car (upright in cradles, facing backwards - with the seat in place & folded down - one less thing to pack) and before strapping them down I lift the front of each boat up & put the MD into the slot, clip it in and attach the bungee to a pedal to keep the fins up under the hull. Works fine. MDs are a b*gg*r to pack in a car - they are an awkward shape which take up a lot of space and don't lend themselves well to lying comfortably on top of other stuff.
I also fill the yaks with all the light-ish gear I can stow (paddles, masts, sails, rods, clothing, fishing kit, camping kit - you name it).
And I put the carts, daggerboards and anything else that's reasonably heavy & low profile on the rear parcel area under the bungees. Have never lost anything yet through theft or bouncing off (touch wood - but I don't think there's any chance that they'd just bounce out or lift out due to slipstream).
Hope this helps