In the Navy, "captain" was a generic term for the CO. I was on a destroy and we never had a real captain (equivalent of a colonel). We had commanders bucking for captain. Nevertheless, they were usually called "captain". As for commodore that was a legitimate rank in the Navy but I think they've done away with it now. but I''ve never heard of a lieutenant being a CO of a ship. By my own experiences, I'd say it never happens.

As far as Clavell goes, I find his writings about Asian, with the exception of King Rat, to be typical white man's colonialist bs.