skipper vs flag captain

skipper and flag captain both are nouns.

Word	Noun	Adjective	Verb	Adverb
skipper	Yes	No	Yes	No
flag captain	Yes	No	No	No

As nouns, flag captain is a hyponym of skipper; that is, flag captain is a word with a more specific, narrower meaning than skipper:

skipper (noun)	flag captain (noun)
the naval officer in command of a military ship	the captain of a flagship
an officer who is licensed to command a merchant ship
a student who fails to attend classes

skipper (verb)	flag captain (verb)
work as the skipper on a vessel