The term, or office, "Chief of the Boat” comes from Submarines. Submarines are boats, not ships, in US Navy parlance at least.
Also known as COB.
In WWII submarines has Chief Warrant Officers who specialized in the workings of the vessel-— their knowledge was valued as the technology changed but also for continuity of the mechanical operation of the warship. The SEALs also have the rank of CWO with specialities to current times. Back then they were known as Underwater Demolition Team-— UDT frogmen.