i am not sure why someone did that, the part of the frame over the axle is at the same height as the top of that crossmember so they havent gained anything.
you can set the crossmembers to be 1.5" tall over the front bed mounts and rear part of the frame and the wood will lay on that crossmember and the flat frame over the axle and you will only lose about an inch of bed depth, plus the thickness of your wood.