I think SBT has hit the nail on the head - there will always be a tension between SOPs and common sense. Attempts to "codify" expertise are not just found in the airline industry - Jeffery Pfeffer authored "The Human Equation" which contains a chapter entitled "Why Smart Organisations Sometimes Do Dumb Things".
He notes that the problem occurs in demanding accountability for a decision or judgement "process" rather than the outcome of that decision. When forced to account for and explain decisionmaking in ways legitimate and comprehensible to a wider audience (e.g. PPRUNE or the regulator) the expert will have to forego any insight or intuition that can't be articulated and will be forced to rely, instead, on the same data and decision process as anyone else. In doing so the expert loses virtually all the benefits of their expertise.
It seems those responsible for the SOPs necessary for operational consistency and regulatory compliance must also recognise and ensure that they protect wisdom, knowledge and competency in their organisations. A tricky but valuable balancing act.
RL