Oh yeah actually ALL these head units have time-alignment capability.... As well as better-than-usual EQ, and they're also all capable of crossing over high enough for tweets and mids, not just mids and sub... so you could go active for a component frontstage if you liked.
What I meant about the 9887 is that it uses technology by Audyssey Labs (MultEQ) similar to some decent home theater receivers like Denon and Marantz for auto-room-calibrate for alignment and freq response correction. Infact, they're incorporating this in quite a few of their 2008 head units but don't know how good it will be compared to how it's implemented in the 9887.
http://www.audyssey.com/
http://www.alpine-usa.com/US-en/products/product.php?model=CDA-9887
Check
crutchfield also at times for different models... good source I think in a lot of cases.. if they have a Hands On Research page for the model.
The burr-brown DAC's in the 9887 I'd say are a clue to a bit better quality in processing and preamp stage, but that's just a guess.. The Clarions just list that it's a 24-bit DAC setup. Other than that it's probably just differences in EQ and crossover capabilities (not counting that running imprint will be THE superior for that)... But the DXZ again has that nice USB input.