Near the end of "The Way to Eden," Sevrin and his group of hippies are not shown running from aux. control to the hangar bay after they paralyze the crew with the ultrasonic frequency. So, we don't know how long it took them to get from point A to point B.
Had the group been shown inside the turbolift going through many deck levels until they reach the hangar bay deck, that would've been a clue that aux. control was a considerable distance from the hangar bay - suggesting a location in the saucer.
Conversely, if the hippies had been shown running through the corridors for a short time (without using the turbolift) until they arrived at the hangar, that might possibly indicate that aux. control was in the engineering hull.