Sure, but the main problem from that perspective judging by the 3rd Interim Report is that according to the book, in the situation whereby the crew consists of a Captain, F/O and relief pilot (i.e. not another Captain) the Captain is supposed to make it explicitly clear which pilot will have which responsibility and also, importantly, determine the parameters by which one is allowed to take control from the other.
The informal nature of the handover after the PNF takes his seat, compounded by the Captain's question to the PF if he had the requisite qualification to be relief pilot (implying this had not been determined earlier, and also according to the BEA implying that the PF is now relief pilot), all indicated a rather cavalier approach to the procedure, so the PNF is quite rightly getting more and more agitated over the handling of the aircraft by the PF after A/P disconnect. Possibly he fears getting written up if he oversteps his bounds - at this point the aircraft is climbing and bucking slightly from turbulence but is not in any immediate danger.
I suspect he initially summoned the Captain not only because of his concerns over handling following A/P disconnect, but also to clarify handover procedure. The report states that under normal circumstances the PNF would have taken on the relief pilot role, which implies that the current state of the flight deck hierarchy is unusual. 2 seconds after "where is he? er", the stall warning sounds continuously for approx 56 seconds, for 54 of which the Captain is not present and the PNF has to process the change in situation from getting written up if he does something he's not supposed to to potentially being in mortal danger if he doesn't do something.
As I said earlier, human factors experts are going to be pulling this one apart for decades. In many ways it's even more complicated than Tenerife, but the ultimate similarity looks to me like getting over the "If I do something I could hurt my career" thought to transition to "If I *don't* do something I could lose my life". The PNF appears to make this realisation 7 seconds before the Captain shows up, but then defers to the Captain on his arrival while the PF continues to make the situation worse. He's satisfied his inital worry because the Captain's here to get things sorted, but in the meantime the situation has become considerably more perilous.
I find myself agreeing with Lyman (whodathunkit?) - the arrival of the Captain ended up coming at a bad time.
Another similarity with Tenerife is that the PNF in this case, like the F/O in the Tenerife case, does not feel he has the authority to physically intervene, but instead tries to resolve the situation verbally while his mind is working through the problem.
AF447 : "You're going up, so go down", "Above all try to touch the lateral controls as little as possible eh"
KLM4805 : "Wait, we don't have our ATC clearance [to PF]", "We are now (at) take-off [to ATC and PA1736]"