The logic here is simple. If you write an app with Objective-C/CocoaTouch (does the same logic hold for JavaME (Android), C++ (various other platforms) and so on?) the user experience created is by that very fact better.
I believe that is the premise to his whole argument, and I find it disingenuous. That is, it's clear to me Gruber meant that a native app with an interface specialized for the particular device is more likely to be better than a web application because the web application cannot have a specialized interface for the device. He is not claiming that making an app native automatically makes it better.