TB, as usual I pretty agree with all of your post. However, I believe that Tom was not captive in the usual sense. To the extent that he was, Tom allowed himself to be captive. I've always maintained that Michael felt no fraternal affection for Tom and that he blamed Tom for not protecting the family. That was why he manifested almost undisguised contempt for Tom as exemplified by the Michale's quote to Tom that you stated.

However, Clemenza didn't live at the mall and only two capos was an authorial device that Puzo employed to keep things uncomplicated.