I've always personally felt that the intermix chamber of the Excelsior roughly matches the layout of the Enterprise refit. Although I do agree that there had been some major revisions with the dual crystal configuration. There were similar discussions about the Constellation class (also with dual crystals - and dual everything else), where the doubling up all main systems was an attempt at boosting performance without necessarily coming up with any innovations. I figure the dual crystals gave the Excelsiors the kind of boost that allowed them to keep up with newer designs later on into the 24th century - possibly implying that they may have had dual intermix chambers/cores.
I'm thinking that the big "hump" where the engines go into the secondary hull was a more structurally sound alternative to the "strong back" configuration of the Connies, taking the pressure of torquing forces off the entire spine and on to a more localized area specifically architected to handle it.