Right now there's a lot of confusion going on between many sites, so trust nothing until someone who's actually been to the show (which Gamespot wasn't) says something.
It's still speculation at this point, but given that SNKP has supposedly been working with Atomiswave hardware since early this year (not counting experience with the DC), this makes sense.
Good news! Although.. What happens if the MVS version is just an inferior port of the Atomiswave version? Will heads explode and water start running upside down or what?