Perhaps I'm being overly cynical, but if their intent was to show what a load of nonsense Apple's insistence that native apps are better is, it sounds like they couldn't have done a better job.
That or the descriptions of the app are somewhat overcritical.
Even so, if Adobe did want to throw a laughing cog at Apple via their clients, they're doing Wired a disservice, and frankly, that's terribly insane. They just couldn't throw a high profile partner/client under the bridge just to amuse some tantric executive war between Adobe and Apple.
Lastly, although hard to believe a company fairly technology agnostic as Wired would use their financial line (their money making product) as a way to experiment with dissing a technology giant, let's pretend Wired and Adobe both wanted to stick it to Apple for the 3.1.3 clause. They would be simply shooting themselves in the foot, as their customer is who really loses out here, not Apple.
It just make any sense at all, although I will give you that it's a romantic idea. More likely, they rushed a replacement implementation, since they couldn't use Adobe's compiler. Conde Naste clearly upholds Wired to the same deadlines as their other high end properties, and want to see a ROI for all the R&D they've had, perhaps. Becausethis certainly looks like a rushed implementation, or at a minimum, one done by amateurs.