Applications must be originally written in Objective-C, C, C++,
or JavaScript as executed by the iPhone OS WebKit engine
This means that any "interactive" elements must either be written directly in Objective C, or you're confined entirely to WebKit.
If you don't fancy building new Objective C apps every time you roll out an issue of your magazine, you have two options.. do it entirely in WebKit or pre-render everything and spew it out with a simpler native reader. Looks like Wired took the latter option. I'd always wondered how magazines would get around this issue - guess we've found out.
I don't really understand your point, can you elaborate? That's all that's being discussed here - native app vs. HTML5 (or some hybrid, which is perfectly valid under 3.3.1).
In an ideal world, your magazine app wouldn't be solely using Webkit, because you might want to create elaborate and performant interactive elements.
However, creating these "by hand" in Objective C for each issue would be time intensive. Instead, you'd usually use a scripting language or a framework like Flash to create interactive elements that are beyond JavaScript's reach. 3.3.1 invalidates this approach requiring you either go Webkit, totally native, or, well, nowhere. There is no middle ground for scripting within apps beyond JavaScript on Webkit.
If you don't fancy building new Objective C apps every time you roll out an issue of your magazine, you have two options.. do it entirely in WebKit or pre-render everything and spew it out with a simpler native reader. Looks like Wired took the latter option. I'd always wondered how magazines would get around this issue - guess we've found out.