Decking=smaller combustion chamber=Higher compression.
However, the main benefit of adding a stroker crank is increased DISPLACEMENT. More vertical travel increases the size of the cylinder shaped mass of air that you are compressing. That is why the Vito's kit comes with a spacer plate. It maintains the compression ratio (more or less) while increasing the stroke. The added benefit of more torque is a byproduct of engine geometry, longer stroke engines with make more torque than an equal displacement short stroke motor.
The fact that some engine builders are putting in stroker cranks without the plate is very cool though. Essentially (I'm assuming) they are modifying the head for appropriate clearance (since the piston prob sticks out of the cylinder) and combustion chamber volume, and certainly building in a bit of extra compression at the same time. With a stock compression of only 6:1 the Blaster has a lot of wiggle room for that kind of mod.
The one thing I really can't comment on is what having the spacer or not would do to port timing. Obviously. having it in seeks to maintain stock timing. I'm just not sure what having it out would do. I suppose cylinder porting to compensate would be necessary, at least.