AFAIK in the Navy the commander of "a ship"-an old Navy vet gave me the definition years ago, I have forgotten it-has the position of "captain" while holding whatever rank he has.
In the 19th Century I think the term "Master" or
"Master of Vessel" was used. Naval ranks developed later than and were standardized later than Army ranks and changed quite a bit-at the Battle of Lake Erie Oliver Hazard Perry
held the rank of Master Commandant.