Yes, the updater-script checks every file that is supposed to be in the system directory of a stock device. Adding files is fine because it isn't looking for them.
Deleting or modifying files like users often do when they root will prevent the update from succeeding.
This situation is most often encountered when users actually want to update their devices and can't because they deleted things without making a proper backup first and/or no fast boot images are available to restore the stock system.

If you are rooted, then managing the firmware on your own device is part of your responsibility as a rooted user, just as managing the security of the device becomes your responsibility when you introduce that level of control to the user, you automatically exponentially increase it's vulnerability.

This is why smart and responsible developers in the community like Koushik Dutta provide the tools to do this with their implementations of SuperUser.