The issue I have with arguments from folks such as Cory is that they presume too much in favour of openness. Many prefer to be regulated rather than have to make decisions on every little detail, that's arguably the whole Apple appeal in a nutshell vs. Linux, and why it's so productive. (Distros like Ubuntu arguably do this too at a much smaller scale.)
Cory is effectively advocating "technology survivalism", where no company will be your trusted for keeping your computers "safe" and "not lying to you". I think it's rather utopian. As far as I can tell, web-of-trust approaches only work in the software world, the hardware manufacturer ultimately has to be trusted to some level, either de facto by consumer belief or de jure by regulation.
Ultimately, his whole premise about "owner freedom" vs "user freedom" may be fatally flawed. It assumes a) Apple wants to control both owners and users to do what they want, and b) owners must be able to control what happens on devices, and this is a necessary precondition to user freedom. I would argue a) Apple just wants to help users with a better experience and b) it's unlikely owners will ever be technically savvy enough to control things, they will always want to delegate things to some degree -- even technical people do this, looking at the number of devs that use Apple laptops.
Cory also oversimplifies the ownership problem. No device owner actually "owns" the software they install, they license it - even with open source. Apple arguably has been the a great force for "user freedom", by constraining what "owners" (i.e. software developers) can and can't do on Apple devices, thus enabling freedoms to the users themselves -- freedom from malware, bad user experiences such as poor battery life, etc. They enable the end user to work around restrictions on content available on the native device by providing a completely open and high quality web browser to get at anything they want in a sandboxed environment. But they also allow the device owner to restrict user actions in the "open web" with (e.g.) parental controls.
Apple's restrictions have little to do with controlling device owners -- they're about improving the user experience.
Clearly the device owners trust Apple today, but Apple could fairly easily move to a TPM-based "certainty" approach where owners get to pick their App Store, if that's what consumers eventually want, and they lose sales over it. But, for now, the market doesn't seem to be arguing in favour of this kind of nuanced approach.
edit: typos