The short answer is "yes". The reason for common rail is better control over the injection event thru electronics and, of course, finer atomization. Common rail allows control over injection amount, timing, and pretty much all other injection variables as a response to feedback from the various sensors - not readily possible with mechanical injection. The computer also monitors and controls intake manifold pressure (boost), transmission shift points (with auto trans), EGR function, and pretty much everything else in the car. The aftertreatment system is there to just sort of clean up what's left.

Almost forgot - the ULSD is just required to keep the aftertreatment system alive. Sulfur will contaminate an aftertreatment system like lead will contaminate a catalyst on a gasoline-fueled engine. The improved exhaust aroma is just a side benefit, though a nice one.

Dan