Those are good points, but there's more to consider.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.
The mount points for the nacelles are completely different on the Destroyer, Scout, and Tug than they are on the Heavy Cruiser. On the Destroyer and Scout there's evidence of nacelle pylon structure in the interconnecting dorsal. On the tug, the support pylons connect to the underside of the saucer. Granted, all those points are near the aft of the saucer, near Engineering. But in the Booklet of General Plans, on Deck 16 of the Heavy Cruiser, there is a section called Warp Drive Engineering near the support pylons that's absent from the Heavy Cruiser saucer. Ergo, the internal arrangement of the Destroyer, Scout, and Tug saucers cannot be either identical or even really almost identical to that of the Heavy Cruiser saucer. This is because Warp Drive Engineering must be inside those saucers, whereas it's explicitly down in the secondary hull of the Heavy Cruiser, and plus there are a few other sections that also have to get crammed into those saucers.
That said, it would be reasonable for all of the saucers to be either largely identical or mostly identical.
TL;DR: The FJ ships do not require or imply that the Heavy Cruiser's Warp Engineering is in its saucer.