The Trek sets were re-arranged as needed to accomodate the production needs, which is how it's done when you have to grind out 20+ episodes a year with limited sets representing a much larger setting. One need look no farther than the bridge and how they sometimes rotated the command module (helm and Captain's chair) to accomodate a shot without a concern for the fact that it might be visibly pointing not at the viewscreen. That's TV.
Extraordinary claims require extraordinary evidence, so if anyone wants to make the case that Jefferies intended the engine room to be in a specific place because of how it was aligned for a time to a corridor set, or that he intended multiple engine rooms when they revamped the set or moved some elements of it around, then it's on them to come up with proof, because what I''m suggesting is standard TV 101 and
requires no expert testimony.