Now that this visualizes what is going on, I have two suggestions, and one wild idea. Suggestion for diagram 1: Why not move the engine room as far back into the saucer as it can be and then make raise the pipes so the pipes extend into the part that stick out for the impulse engines? We'd get a close-to full height room in the "right" place with only a minor set alteration. It looks like the room itself, at least, would fit there. Suggestion for diagram 2: If the Engine room is in the tall part of the saucer, why not move Engineering up one deck, to Deck 6, and then the pipes can extend all the way to connect to the impulse engines? Wild idea: What would the size of the ship and deck height need to be for a 14 deck saucer? That would allow the idea of "decks" and "levels" being two different things, and yet match what was on said onscreen. Better yet, what would the size and deck height need to be for the ship to have only 14 Decks total?