Re: I would not store critical configuration data in a config file.
I when I read that statement in the story I interpreted it as:
Because of variations in manufacture and the tight tolerances of the flight, during installation certain bits of information specific to this engine on this plane are set and recorded for use by the system. So the data will be different for each engine.
How other than a"config file" are you going to store that data? Yes you can argue there should be safety mechanisms to prevent it being inadvertently overwritten, but depending on what else you are updating you might already be in a privileged context anyway.
Yes, I think a check at start up was in order, although in this case it should flash a warning and ground the flight, not supply some default that may cause the same sorts of issues later during flight anyway.