I was just referring to the Equinox episode of Voyager, I'm sure there's other protocols/orders which can take priority.
Would that protocol still hold for ships from different eras, though? In that case, probably Captain Nobody from Manure Hauler #4747 with a total crew complement of 3 and near to zero combat experience from the 31st century could still have a vessel tactically superior to Kirk's enterprise and outrank him ...