Honestly, I've been wondering this myself ever since the 3.6L was offered in a Challenger. I mean, I have no doubts that a lot of it is in the computer but I really would have thought that Mopar would have offered some kind of performance kit for the JK by now.
I thought the same thing about the difference and was told by a mechanic at the dealership that it's because of the air intake system, slightly more aggressive cam grinds, and less restrictive exhaust......I found this bit of info that backs up the air intake part of it......
http://www.pentastars.com/engines/tech.php
"Despite the four variants of the 3.6 already being sold — rear drive (290 hp), AWD (292 hp), FWD (283 hp), and Challenger (305 hp), there are just two head designs, two intake manifolds, and one set of internal components, including cam and pistons (this probably changed when they added the Ram setup, 305 hp, though the rep said the main advantage in the Ram was the space available for the exhaust), according to an SAE article by Paul Weissler. The Challenger's 13 horsepower increase is due to "a more aggressively designed intake air system" which increased airflow from 214 to 220 g/s."
~Woodrow~