I just tried placing the engine room in a 1000' TMP E where the impulse engine is and it doesn't fit. (Vertical shaft lined up the dome.) The top level sticks out of the deflection crystal dome by 6' and the lower deck platforms stick out of the neck by a foot or two on each side. Also, the side corridors in front of the foyer of the blue corridor stick down from the undercut. And lastly, the horizontal conduit room in it's forced-perspective form also sticks out of the bottom of the impulse drive.
On a larger 355m ship, the top of the upper level sticks out of the dome by 2'. The sides of the lower decks stick out but by a much smaller amount. The FP horizontal room now fits barely in the impulse engine space but the two diagonal conduits leave zero room for space behind the orange glow grills.
In both cases, all space at and to the aft of the vertical shaft is unusable by turbolifts and you'd have to fit all turbolift cars in front of the vertical shaft decks.
So as interesting as placing the engineroom as seen up where the impulse engine/neck sounds, it doesn't work and causes way more problems than it solves in it's current configuration.
Edit: Unless there is more useful data regarding set sizes I'm putting this to bed and won't revisit it unless something new comes up.