I believe that there are two other differences with the BA system. It's my understanding that the system has-
-Crossovers, The door speakers don't play the highs, and therefore are strickly mid and bass, which they are good at.
-Amplifier, The BA System has an amplifier for the remaining speakers, allowing for cleaner-high-volume play.
Those make big differences in sound quality.
Also, as someone with both systems (base on compass, BA on pat), I can say that the base system is GREAT compared to other base cars. However... the BA is superior, especially at high volumes.
Yes, you can have a better system for a lower price if you do it yourself, but probably not by much, and the amount of time it will take to make it look cosmetically good is rediculous.
Your going to have to put in two tweaters, rerun wiring for 4 door speakers, to an amp, which your going to have to find a creative place to put so you cannot see it, replace the four speakers, and either custom build a box to fit in that spot, pay $400 to buy the BA one from chrysler, OR put another clunky sub box in your trunk. Now merely to maintain the same BA quality, I'd estimate $200 for the amp, $200 for six speakers, $400 for the BA Subwoofer, and 10-12 hours of your time, plus its not under warranty, and making it look good will be a lot of creativity...
I say, unless you are an ultra-audiophile, who truly wants "the absolute best", the BA is the way to go. If you are an audiphile and can tell the difference in quality of sound, and/or listen to high volume play, go with the BA, and if you can't tell the difference (or dont care) between a counter top stereo and a full bose system, go with the base.