O/T I think there was to be a Captain of engineering with whoever sat in the chair being a Commodore at least...
There wasn't going to be a Captain of Engineering per say. In TSFS, Scotty was ordered to report to the Excelsior as Captain of Engineering. But lets examine the evidence, Scotty was wearing Commanders Insignia in that scene, when we next see him on the Excelsior he is wearing Captain's Insignia.
So it was more likley he was being promoted to Captain and reassigned as Chief Engineer of the Excelsior. Who knows following the shakedown crusie he might have been reassigned elsewhere and a new CEO assigned with a rank of Lt. Cmdr or Cmdr.