The problem with this theory is that there was never any canon evidence of the change. We never saw a one-pip Admiral (or Commodore) in the 24th century. The only evidence is in non-canon "reference" books like the Encyclopedia, and the Memory-Alpha site (which takes that info from the non-canon "reference" books).
Personally I'd love the progression to be Captain, Commodore, Rear Admiral, Vice Admiral, but as I said above, if it's not happening there has to be a reason it's not happening. Heck, Cryptic is spending time to make BO's First Officers and Captains of their own ships because players want them. A simple thing like the Commodore title, much asked for by the fans, wouldn't be out of the question without a good reason.