package manager updates vs software updating itself

Obviously distrobutions have their own methods for updating the software you install on your system via their package manager. However, if you install a piece of software locally, it'll usually have some function to check for and download/install updates itself. When you install something through a package manager, the program no longer does this since the package manager is going to handle that to keep the system consistent. I get all that, but.. What is the process for disabling that piece of the softwares behavior? Is it generally done through modifying the code? How would that work on closed source software? Or is it usually just a matter of changing the default preferences to not do this automatically? If that's the case, could a user end up with an inconsistent system by reenabling it? I'd be curious to know what that process is like for the people working behind the scenes.

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