Making flag rank is political as much as competence in military or naval arts. Being a Colonel or Navy Captain is like being a fighting brown belt martial artist instead of the teaching black belt rank.
Unless something has changed the US Navy doesn't really have Commodores, except as a convoy commander title. Just lower half 2 star Rear Admirals. Some say it is so they always out ranked the USMC Commandant which was a "mere" 1 star Brigadier General until WWII.
well from what I under stand the commodores are still being used in places like budds training camp. as the heads of schools for Navy seals. I've seen as much in their training video's and looks into the schools & interviews too.
I've seen them more in use then that of commandant's which I've see only used in police acadamies these days and since the 80's til to day. as for tv it's just deep space 9 and I have't seen it since. un less it's a civilian police related deal these days.
Now as far as these shows go of the show NCIS that was this past weekend's with NCIS L.A. where the was female commodore who was the head of something similar to what known as "think tanks" are used used think up idea's for planning of terrorist attack's and having alternative plan's for emergency . she called it a brain trust cause miltarty has their own words for thing campare to civilan agencys.(<< or other's like Cia)
that Commodore turned out to be traitor selling out to Russian agents and this was just after Kensey and Deek's returned from their honey moon and it was about nell's sister(who works for NSA) and some one they went to school with the latter of which was in the navy and is geek.
it seem's they 're (<<Commodores) still in use in other ways despite what's written in the books we look up. I always had a feeling there's something between captain or fleet captain & commodore or should be. but the say other wise.
I know there's Such a thing as a Adjutant in other part's of the military and if that head of the base is fit to command that Adjutant takes over. not sure if that what's supposed that for the navy.
They should probably just have commodore equal colonel. some else for major if there isn't one & they can still have their fleet captain which our just captain of ship flag or not .
but I may be thinking about this too much.
it's possible harm just refuse the promotion or got himself demoted like startrek's orginal kirk some how .