Ultimately it's up to the skipper of the boat to interpret his orders in any way he sees fit, as he is the one most aware of the tactical situation at the time.
This is one of the themes explored in the movie, Run Silent, Run Deep, when Clark Gable takes his boat to the Bungo Strait despite having been given specific orders to avoid it, claiming that he is in possesion of new facts which give him a tactical advantage that HQ is unaware of, thus setting up the conflict with Burt Lancaster, his XO. It was also a theme which was rehashed in Crimson Tide Between Gene Hackman and Denzil Washington (nowhere near as good though).
One of the critical things with military doctrine is that a battle plan survives intact about as long as cheap screwdriver does. This was one of the problems with the former Soviet Union, where the officers were vastly more skilled than the men, meaning that if the officer took a hit, there was rarely anyone below him who could take over with any degree of competence. More enlightened forces place the emphasis on everyone being capable of taking the initiative and training the man below you to do your job, which is why conscript armies usually get their asses kicked by volunteer forces.
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