I admit to being a merely SLF, but I think you guys are making a meal out of this. I do not see how it is so difficult, given the evidence now presented, to come to some fairly straightforward conculsions.
First, it is clear that the investigation has been well handled and no expense has been spared in gathering evidence in order to understand what happened.
There is no evidence that BEA or any other party is manipulating the evidence to promote, or protect, any other party.
It is clear that in a modern cockpit, when things go wrong, the independent software streams are capable of presenting the human beings with an cachophony of instructions, advice and warnings.
There is no evidence of unwarranted presence on the flight deeck.
Training, and modern concepts of technology, give a basic belief in the security of systems.
It is easier to explain, by way of repetition, the capabilities of a system designed by humans than it is to explain the workings of the physical universe.
If circumstances project you into the gap between your training and reality, you need a more fundamental understanding than your training provided.