The first thing I wondered after reading this article is whether there might be a scheduled task to run the permission reset similarly to how the author ran it via the command line.

It seems most likely that this is some kind of bug where that command or its underlying actions should be called every time the user unchecks something in the settings panel.

This is what we get when the iPhone’s permission system is grafted on top of a desktop OS that was never designed for it. I think they could have done something that is more Unix-like and yet friendly to the GUI end user.