The flat-deck handles better at high speeds. The cross section to the wind, and the center-of-gravity being lower are the main differences there. Also a little less weight. The raised deck has 6'10" of headroom at the back of the cabin, tapering to right at 6' at the foot of the bed. My wife is 5'11" and can walk all the way forward and not bump her head. The flat deck is a little less than 6' I believe.
Steve David had his for a few years and regularly took it to the Bahamas in some of the roughest stuff the Stream would throw....