Most definitely....your wax works with your base. All decent snowboard manufacturers have sintered bases...the difference is in the molecular weight. You'll see numbers like 3600, 9700, etc. Those numbers represent molecular weight. The heavier the molecular weight of the base is, the more it will absorb the wax as the molecules are bigger creating more space between them allowing more wax to "infuse" into the base; therefore creating a better glide. Home waxing is very easy and I encourage you to wax as often as you can as it will end up being alot cheaper for ya. If you know how to iron clothes...you'll be able to wax a board.
As far as flex is concerned i would say that the GNU SS has a touch more flex to it. Any particular reason why you ask?