That makes sense to me.
Actually, not only do I agree, but the idea of multiple engine rooms would be great as it solves both dramatic and technical concerns like you said.
But this opens a whole new discussion that I frankly would find fascinatingnot to mention it ties well into the original post: Is there any way to tell from each episode which engine room is being shown, the saucer one or the secondary hull one?
Well a lot depends on your “in-universe” interpretation, as to whether the 1st and 2nd/3rd season engine rooms both stayed the same throughout the five year mission or whether both looked like the 1st season version with minor variations and then were both redesigned to look like the 2nd/3rd season version with only minor variations.
Another possibility is that there are actually four engine rooms onboard, two in the primary hull with one like the 1st season version and the other like the 2nd/3rd season version –either side by side, or end to end and aligned transversely to the centerline axis of the ship and so sharing a tube chamber between them; and then two in the secondary hull with one like the 1st season version and the other like the 2nd/3rd season version and most likely back to back sharing a tube chamber (which is not the engine per se but just some kind of power distribution manifold).
The one(s) in the impulse area of the primary hull would be the “Engineering Section” the one(s) in the secondary hull would be the “Engineering Deck”.
P.S. Some episodes just use the generic term "Engineering" without specifying whether they are in or near the “Engineering Section” or “Engineering Deck” so in these cases we need to look at the overall context of the episode as well as the dialogue for clues that might help clarify (or fudge) the location in question.
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