I suspect the Haynes Manual will try to fit what we saw on screen, and hopefully elaborate on some in-universe design history.
When I think about the way Engineering looked in TOS, I find that the multiple-warp-chamber idea was a good one, and fit in with TOS in a subtle way.
In TOS, we never saw the ertical/horizontal columns one would expect from a central Warp Core, pointing to a potential alternate arrangement and configuration.
The Engineering section seen in the movie makes sense in general, but I would love to see something akin to these designs.
I love the idea of looking through to the Navigational Deflector, and having a crewman looking out at an unknown phenomenon would be absolutely epic.