AARRGH! The small details escape me quite often. You're right, two distinct engine rooms. My question would be then; is there any point in having an independently controllable secondary hull in TOS? The weapons are all on the primary hull, so it would offer no tactical advantage and the primary hull has more than enough room for the entire crew to serve as a lifeboat. So would there be a reason to have a crew there to pilot it after a saucer separation?
You make a good point, from a defensive point of view. The only real advantage a "skeleton" engineering crew left behind in the engineering hull would have is they could escape at warp speed, whereas the crew left in the saucer would only be able to trudge along on impulse power.
On page 191 of TMoST, Whitfield describes one of the features of the engineering hull: "Minimal crew quarters are located in this hull, used by duty engineers and by the star-drive crew when the saucer section has detached and is operating separately."
Perhaps the reasoning behind this would be for the "fastest half of the ship" to reach the nearest star base for help.