'throughout the flight, the movements of the elevators and the THS were consistent with the pilot’s input'
BEA Third Interim Report
In other words, the motions of the control surfaces were consistent with the pilot's control inputs (i.e. no unexpected control system inputs)......but that says nothing of the dynamics of what the control inputs did to the aircraft. From the same report's data, it also appears to have set up a roll oscillation.
OC, What you do not seem to realize is that the Aristotel paper builds on a long history of professional thought on the causes of PIO. This is not a report that just "appeared out of the blue".
That is not an assumption that PIO can be designed out of a particular aircraft's control system-you can take that as a fact, but first it has to be recognized so that it can be addressed. Pilots who blame themselves for
all aircraft handling problems are one of the reasons not all PIO problems are addressed.
I will concur that the crew of AF447 seemed to be clueless about a large body of fundamental aviation knowledge that night, but I suspect recognition of a PIO context for their initial manual control performance will explain how they lost control. It may even help explain why they failed to regain control, although the aircraft was then in a stall and no longer subject to PIO. But this area is one for the human factors experts.