The app store being incompatible with the GPL is really the choice of the writers of the GPL and those who use it as their license. Other open source licenses are not incompatible with it, it is just the GPL that chose to be.
Moreover, you didn't even address the point that Apple makes it increasingly difficult (and sometimes even impossible) to distribute code for their platform without the use of their proprietary SDK. That, of course, is an artificial requirement by Apple, yet again signiling that they are not friendly towards free softwre.
Note that, a hostile environment for free software does not mean that there is no free software or that free software is impossible. If that was the case, I would've used that wording. It's hostile because it makes it harder for free software to exist and because it does not integrate/cooperate well with free software.
Anyway, user freedom is the main point of free software and, supposedly, of the original article. In that sense, it's hard to argue that Apple ranks any higher than even MS.