A few questions.
Was the P-B-D inserted into the primary flt plan, the secondary, or both? At what point exactly was the secondary activated?
Did the a/c have TERR ON ND function? If so, was it displayed? And if so, which ND? Was the radar on? Displayed properly? Which ND? And at what tilt?
Without knowing answers to these questions (and others, I am sure), we will never know what exactly happened, let alone why.
But from the transcript, it seems that something was stifling the FO from alerting, challenging, and ultimately taking control of the a/c. My guess is that the flight deck atmosphere was about as poisonous as that of G-ARPI, which Stanley Key presided over. And the old chestnut of abusive captain's incapacitation was raised in that accident as well.