My theory on Como. Decker and Constellation
-- which I've stated before so forgive me if it sounds familiar -- is that four starships form a cruiser division (to use a WW2-era term, you may prefer squadron or group, whatever). Three are commanded by captains, but the fourth has a commodore who has a second hat as division commander. Since starships normally patrol alone, the commodore usually acts like a normal starship captain, aside for some extra paperwork as division commander. But if the division is assembled to act as a task force, as in "The Ultimate Computer," the commodore is in charge and his ship is the flagship.