Your link doesn't say that there isn't a clear chain of command, it says that there should be a culture that allows professional disagreement or calling to attention. Just because the captain is declared top dog doesn't mean that protocol demands subordinates must remain quiet.
BTW, who is commanding the plane (by inputs) and who is commanding the crew are entirely separate questions. I think one of the serious issues that MUST be addressed here is the issue of conflicting commands to the plane.
Two options....
1) Place all controls between the pilots so they can easily see what eachother is doing or
2) Place a selection switch and indicator that allows a pilot to unambiguously take control of the plane and disable the other input, or to keep them in linked mode where they move together and provide tactile feedback as to what the other input is doing.
Then they have to fight! You can't delegate responsibility to the "system" to resolve such a fight. A fight is a fight. And if it's happening, you can't automagically get rid of the fight.
At least there's feedback, and you can immediately see what's happening! In the current configuration, Bonin's stick inputs were nearly unknowable to the other officer.
Yes, the link doesn't say that, but research further and you'll find that the concept of a hierarchy is what CRM aims to eliminate. It's the First Officer's job to take the flight controls from the captain if the FO thinks the captain is doing something dangerous. Not to ask for permission, but to immediately do. This goes against the concept of a hierarchy, but is why they put two sets of controls up there.
I think you'd still do better to have a manual selection of which input is commanding, with an option of having both sticks linked and moving together.
