"...now you are making for a longer wavelength by causing frequencies to travel the distance to the back and then to the front of the car..."
Think about that for a while and you will see why it cannot be.
The real deal is CANCELLATION. The woofer generates a wave and it radiates in a spherical pattern about the box unless blocked by the floor or whatnot. This means that a wave travels toward the front of the car and toward the back of the car at the same time.
The woofer travelling to the rear is the problem. It will reflect off the back of the trunk (nowhere to go right) and head toward the front again OUT OF PHASE compared to before it reflected. When it reaches the same plane as the woofer it will now cancel out the frequency that corresponds to the wavelength from the baffle to the back of the trunk. Make sense?
In most cars when the woofer is against the back seat the frequency corresponding to the distance from the seat to the back of the trunk is in the 70hz range and you get cancellation at 70hz. This is an important range of music for your woofer and you WILL notice it missing.
Turn the box around though and the cancellation frequency goes up to 130-140hz and is above the woofer's range. Problem solved.
As Chaos alluded to, if you totally block off the trunk from the cabin of the car then this is a very small or non-issue. Aside from looking fricking deadly, that is the sole purpose of the baffle shown here:
http://images.cardomain.com/member_i...882_5_full.jpg