It's been rather disturbing to see this whole thing play out --- I'm not taking sides here, but Apple "flexing its arms" in this manner shows that it is willing and has the power to go beyond policing its App Store and such (which while I do not like, I feel it does have the right to) and involve itself in the affairs of third-party software which it did not originally install. (This is subtly different from updating…
any OS (and many other apps) that update have the power to do what you’re afraid of, and much more.
plus i don’t really see a bright line between system level software and an app when apps can access your video cam, mic, all your files - basically your whole computer.