Bless you Attila, for saying it so well, "At the end of the day, though, as in this emergency with the SAR S61, the captain has the overriding authority to make such decisions as he sees fit."
This is not carte blanc to do whatever, but it reminds us that the checklist is an informed guideline, not a set of handcuffs. Picture captain Jean-Luc saying, "Romulan Battle Cruiser at 2.5 parsecs? get out the Romulan Battle Cruiser check list!"