Remember, the Kenwood's CD interface was designed to deal with a CD changer - including power for all of the mechanical parts that move the CD's around. That is more than enough power for a laptop hard drive. I really believe that the engineers knew what they were doing when they made that choice, and that Phatnoise was aware of the power issues as well.
I'm also pretty sure that Kenwood was pretty clear on what they did and did not want to include on their branded "Music Keg", which led to the elimination of the additional power jack and the RCA inputs as well.
Another thing to note is that using a seperate power source/path opens you up to all kinds of grounding and induced noise issues.
On the other hand, if you are having problems caused by the power feed from the headunit to the phatbox, it will probably be a lot of fun (not) tracking it down.