Rick Berman originally wanted a new filming model built for the Enterprise-B. Allegedly, he was tired of constantly seeing the Excelsior class in TNG, despite the 'Enterprise history wall' seen in the first few seasons showing a regular Excelsior representing the B (and it's not like the C on that wall looked anything like the C filming model either.) If this had happened, then the original Bill George Excelsior would have probably made one last appearance in VOY's "Flashback" before being permanently retired (rather than Jein making a new model because of what happened to the original one in Generations), and the new B model built for Generations would have been the 'guest starship' in DS9, and we wouldn't have the discrepancy which you describe. Of course, this never happened, so we have no idea what that version of Berman's Enterprise-B would have looked like, as I don't think it even got to the concept art stage before the decision was made to use the Excelsior with add-on parts.