You are absolutely right that the Carbon/Cocoa distinction needs to be explained differently. The view of the APIs on top of each other that I presented is simplistic, as is the view that they are parallel. There's actually a lot more going on than either of those views show. As I move through the conference I do find myself flipping between the two.
As to OMNI being critical of Carbon application development, well, of course they should be. They've done a lot of amazing work in Cocoa and they deserve a lot of kudos. Please don't misunderstand my article as a vibrant support of Carbon. I'm a big proponent of Object-Oriented technologies and my current opinion is that new development for OS X should either be done in Cocoa or in Java Swing. But, knowing that Carbon's functionality is being used in both cases is good to know from the standpoint of understanding the system.