That's because you're a civilian and you don't understand how Naval Aviation works. Reading straight from the NATOPS manual for my old aircraft: "It provides the best available operating instructions for most circumstances, but no manual is a substitute for sound judgement. Operational necessity may require modification of the procedures contained herein."
Aviators are not expected to be checklist-executing drones who "follow protocol." They are expected to have an encyclopedic knowledge of their aircraft's systems so that they know when to follow procedure, what the procedures are designed to do, and what to do when they have a situation where the existing procedures don't apply or conflict with each other.
In my old community, it was a commonplace occurrence when requalifying in the simulator for instructors to deliberately insert situations involving multiple malfunctions whose emergency procedures conflicted with each other, such that blindly "following protocol" would cause you to die.
Aviators are not expected to be checklist-executing drones who "follow protocol." They are expected to have an encyclopedic knowledge of their aircraft's systems so that they know when to follow procedure, what the procedures are designed to do, and what to do when they have a situation where the existing procedures don't apply or conflict with each other.
In my old community, it was a commonplace occurrence when requalifying in the simulator for instructors to deliberately insert situations involving multiple malfunctions whose emergency procedures conflicted with each other, such that blindly "following protocol" would cause you to die.