The idea is the amount of air you have to push... in a trunk you get a lot more distortion by firing into the seats and you get a weaker sound to begin with. By firing into the seats you are forcing the air directly through the seats, but it expands outward and goes up through the rear deck lid causing the sound to be broken up and distorted. By firing into the trunk you have a larger area for the sound to reverberate (right term?!) in, producing a fuller sound and more volume.

In my hatch I have the sub facing the rear as well, because with the seat up it sounds no where near as clean...