Perhaps PastryKit was developed originally as a "plan B" in case the
    App Store didn't take off. Its development probably tracks back
    to before 2007, when third-party native development was still in
    question, and was kept in the back pocket as the App Store
    was launched.

Actually, given the history of 3rd party development on the device, I think this was "Plan A" and the App Store was "Plan B." When you watch the first couple of Stevenotes that came during and after the iPhone's public announcement, you'll note that Apple was originally expecting developers to only make web apps. But there was a big push-back from developers complaining that they couldn't make apps good enough to stand side-by-side with the built-in ones. (And people also pointed out the pointlessness of advertising to devs that the iPhone was using the same technologies as OS X if they couldn't be directly accessed.)