PJ2,
When trying to understand this "things" we must remember they are "complex feedback Systems" eventually with crew actions affecting final results (crew with his own feedbacks not always logical and understandable by us).
Many years ago i worked (Testability of complex electronic Systems) in diagnosing "complex digital circuitry" full of feedback loops. The only way we found adequate to diagnose a faulty circuit down to the component level was "to open the feedback loops" at least, momentarily.
The simple reason is: When there is a certain failure, the "feedback loops" make the "failure" appear also in the inputs of the System. And this was for a Hardware in a lab, in a bench with all necessary stuff (Digital storage scopes, logic analyzers, recorders, etc.)
When investigating incidents (e.g. AIRPROX) or accidents (AF447) i suspect the current FDR´s may be not are enough to provide all the required details (e.g. the WRG fault) to allow a definitive conclusion.