I'd imagine that a lot of the undocumented stuff was for things that were obvious to an engineer at the time -- I doubt many engineers working on it at the time thought that the probe would outlive their own lifetime.

I've run into lots of software comments in legacy code that refer to features or systems the company used to have that were deprecated years ago and are nearly meaningless today. Knowing that a flag was set to match the flags from the WOPR sytem isn't that useful when WOPR hasn't existed since before I joined the company.