I'm from a different industry, but I think there are parallels. We design large and complex oil and gas plants. During the design process we spend literally thousands of hours developing the safety case for the facility, and thousands more hours documenting the design. We then develop procedures that describe how the facility is intended to be operated. The safety case is embedded in the design, and the design reflects the safety case.
However hard we try, I have never seen a documentation set for a complex plant which accurately captured in an assimilatable form all the underlying thinking of the designers. We tell the operator how we expect him to react in a given set of circumstances, and try to make his decision process as simple and intuitive as possible. To keep it simple, we do not try to explain in detail why it is the way it is: the reason you need hundreds of specialists to design the thing in the first place is that one person cannot understand all of it.
It never ceases to amaze me that the operators of the plants we design are quite happy to tinker with the immaculate conception almost on a whim. The more 'sophisticated' the operator, the more likely this is to happen. In my experience, he will invest roughly two orders of magnitude less effort in changing the operating procedures than we spent in developing them. Either he is very smart, or we are very dumb.
I would suggest if you buy a commercial jet from someone like Boeing or Airbus, there has to be an underlying assumption that they know more about how it is intended to work than you do. Rewriting the SOPs is then both high risk and arrogant: if the SOPs are wrong, make it safer for everyone by making your case for change to the manufacturer. If you change them on your own, ultimately, the law of unintended consequences will catch you out, and something, maybe people, will break or get broken.