There is a short list of things that will drastically effect the frequency response (transfer function) of a sub in a vehicle. The short list is as follows in order from most prominent to least.
1. Boundary effects caused by the sound waves reflecting off of the interior surfaces of your vehicle (back wall, wind shield, ceiling, floor). For more info checkout http://www.trueaudio.com/st_spcs1.htm . Due to the large size of sign waves in the bass range (100 Hz = 11.3 feet and 20 Hz = 56.5 feet long) the boundary effects exist everywhere in any vehicle. In other words at all points in side a vehicle the sound level potential is drastically increased due to the waves having to bend and consequently multiply themselves.
2. Cancellations. Cancellations can virtually eliminate sound at a given frequency, (despite boundary effects, multiple speakers, or massive power) caused by an emitted wave encountering a reflected wave (coming from the front of the vehicle) that approximates 180 degrees of phase difference. As frequency lowers the probability of this occurring increases in the event that the sub is located anywhere other than the far front or the far rear of the vehicle. As you approach the center of the vehicle the range of effected frequencies expands. This is a mathematical fact.
3. Multiple acoustic resonant chambers (trunk, passenger compartment, etc.) interacting with each other.
4. Lossy boundaries such as flexible ceilings or door skins (defeating boundary effect gains) are frequency specific and non linear. Thus they must be measured and not predicted.
These are the four most basic acoustic rules to follow when engineering a subwoofer for a car. There are many more complex effects and calculations that can be made but all are dwarfed by these four. There have been many great systems produced where the sub was not located in the far front or the far rear of the vehicle. These vehicles all perform in spite of this fact not due to it. There are many valid reasons why an educated installer would locate a sub in an area other than the far rear but all instances include a substantial compromise in subwoofer output and consequently quality. Since the sub must physically move more air to make up for this loss and consequently produce more distortion as the voice coil leaves the most dense part of the magnetic flux.