in general, you do want the port and cone close, you do want the rear wave to combine with the front to create one new wave - not two separate waves that have to combine later. the port length is what allows the rear wave to travel a further distance and be in-phase with the front wave.
think of it in terms of path length. visualize or calculate the wave (peaks and valleys). wavelength is 1125ft/sec divided by frequency. when a rear wave travels 1/2 of a wavelength (at a particular frequency) it is now in-phase with the front wave.
putting the port at the rear increases the distance travelled by the rear wave (before it combines with teh front wave) and thus can lower tuning frequency.
the concept of "loading" is just taking advantage of reflections as soon as possible so they too are in-phase with the original. it's why putting a sub in the corner of a room excites all room modes.
and room modes... that's another subject entirely.
just think that if all of this goes into the placement of one sub and one port - how much more complex the system becomes when you have multiple subs and multiple ports?!? when you have different path lengths from each sub to the port - they are effectively tuned differently and they will interact before they even have a chance to leave the port. it becomes very complicated very quickly. i believe simplicity is king, install is 90% of the success, and the vehicle is the weakest link.
some of this is stuff i have read in textbooks, but most is just my thought process in how i'm trying to understand these very dynamic, non-linear systems. i could be wrong. but i did stay at a holiday in express...