I would assume that the intention of the scriptwriters was for the main reactor itself, aka the energizer as it was repeatedly called in the film, to be closed off in a separate, radiation-shielded room. However, due to the film's low budget, they couldn't radically rebuild the existing engineering set to fit the script, so they best they could do was stick in that little booth on the side of the existing set and pretend it had something to do with the engines.
Since the "main energizer's out" and Scotty said the "energizer's bypassed like a Christmas tree," maybe the booth in engineering was an auxiliary access point for the system, and there's a more elaborate room off somewhere else.