(a) Notwithstanding anything contained in the Rules 4-18, any vessel overtaking any other shall keep out of the way of the vessel being overtaken.A vessel being overtaken is the stand-on vessel. A vessel who runs down another stationary vessel is also at fault, especially if the vessel underway is not a "burdened" vessel (e.g. unable to stop and/or restricted in ability to maneuver due to size/draft/narrow channel etc.)
So, if these guys were fishing in a narrow ship channel and they don't move out of the way of a 500 ft. container ship they'd be at fault. If they were run down by a maneuverable pleasure boat that could reasonably be expected to have the ability to avoid them, they would not. The small fishing boat is not "restricted in ability to maneuver" in that situation.
OTOH, if they had broken down and were unable to move, and had called a Pan-Pan before getting run down by a large ship, then I'm not sure how a court would rule. Or, what if they hadn't called a Pan-Pan? Probably, either way more factors would need to be considered and it would be a complicated case.
The overtaking boat was under command, negligent command. Looks like not under command is reservef for "exceptional circumstances", like the autopilot was remote controlled by a psychopath and if it was turned off the boat would explode, or the skipper was dead or something like that.