I'm not entirely sure what you mean by "part of operating system, separate from the app stores", but in this case a server was delivering tainted updates, so ha

I'm not entirely sure what you mean by "part of operating system, separate from the app stores", but in this case a server was delivering tainted updates, so having an OS-based update mechanism/package manager by itself wouldn't have prevented this. Unless you also mean that this update should have gone through the OS's repositories (which I feel is close to app store).