First off, the article's biggest point, the security sandbox, is not the issue at all with the App Store. The entire internet runs inside of a sandbox.
Developers understand they must play fair on a device that is shared with other developers. I don't think I've seen anyone complain of this anywhere.
However, what Apple has employed its engineering team to do is create and enforce only one path to getting usable apps on the device and that's through installing via the App Store.