Not to totally nerd-up this sentance
...But I used to dabble in audio stuff...and this is almost the same basic theory behind mono and stereo sound systems. It has to do with resonance, specifically in this case; pulses of air.
Each bank of cylinders has four exhaust pulses per every two revolutions. In a true-dual setup, this allows those pulses to come out the tailpipe largely unmolested. So you can actually hear those pulses if you listen carefully. Consider the fact you have two banks setup like this, and you get this beautifully clear, deep, rumbling exhaust note like the Mustang. Now, somebody's going to say "the x-pipe links the two together, so what's the difference?" The X-pipe helps to equalize pressure in both pipes (or the strength of the pulses). But the resonance itself still makes it through.
If you route both banks through one pipe(like the 4th gen)...you get 8 pulses per two revolutions. That's double the amount, making it difficult to detect the rumble. On top of that, though, they interfere and hit into one another as they get slammed into the same pipe. This messes with the resonance, and results in the sound getting 'smoothed' out, because your ears cannot detect the separate pulses anymore. As far as sound goes, it's still deep, but it's no longer clear, nor rumbly.
Thank God for a 5thgen with true duals.
