It occurs to me that IF the FJSTM ships were canon vessels it would make sense to have engineering in the saucer as those ships do not have secondary hulls. The warp core could be vertical, and located in the neck.
The two round pods on the floor with the dilithium crystal between them, called the "Impulse Syncrotron," could be the top of the warp core, like the Impulse Deflection Crystal would be on the refit. Then, the blue structure that takes its place in TAS would be an expansion of that system, moving towards the Impulse deflection crystal, and the Dreadnought would connect its upper nacelle to the warp core through that structure.
The season 1 engine room could be the one near the horizontal part of the warp core, sort of like Drexler's diagrams, hence no Impulse Syncrotron on the floor. And, it kind of looks like Warp Engineering from the FASA blueprints.
I've always been an "Engineering is in the Secondary Hull" guy, but this kind of convinces me to consider it the other way.