So this was one of the things I asked Raja specifically about. The reason for the M.2 riser goes as this: this is an overclocking board intended to support liquid helium cooling down past -250 degrees. Therefore, you have to be careful with component placement, and they wanted to keep the M.2 cards off of the board. The use of a DIMM slot solves several problems: first, the number of I/O pins let them do straight traces to support two M.2 cards without the need for quick switches; next, the position of it lets them use, as double duty, the memory cooling fans as fans for the M.2 cards; DDR3 slots are dirt cheap, so it is inexpensive; and finally Raja noted that the feature has generated a fair amount of marketing buzz.
So I respect the design decision. Could they have done something else? Sure, but it is an interesting solution to the problem.