There is no reason to believe that rank titles will not continue to evolve in ways that we might not predict. A good example is the Royal Ar Force. A "squadron leader" does not command a squadron today, it has just become the term for that particular rank. It's been around for almost a hundred years now and causes no confusion or difficulty, everyone is used to it.
If we stay in-universe, you have an argument. If we go meta-universe, when Roddenberry conceived it, he deliberately stuck to forms and structures his audience would be familiar with. Essentially, it was a dramatic re-creation, so likely most of the adventures happened to other people in-universe, but Kirk/Picard/et alia were the meta-characters we saw and related to. Similarly, while "Captain Picard" was our vehicle for viewing the 'verse, in-universe he was a conflation of Ship-Leader Grantham, Scout-Commander Renaille, and Roving Federation Agent T'Shirr, depicting the adventures of those three and dozens of others - kind of like how Hornblower, Aubrey, Drinkwater, and Bolitho are pastiches of various real Royal Navy officers, and their adventures are frequently drawn from actual logs of the napoleonic age.