Well, here's my two quatloos worth. In the case of the original refit we should respect the designers intent, but the E-A obviously has some major internal differences so anything goes? As for the deflection crystal, that's something that the vertical intermixer/warp core can,
but does not necessarily have to,
connect to? Also, here's a thought, might the reuse of the TNG engine room suggest that what were seeing here is actually the top
of the warp core, near the impulse engines? It looks somewhat like what was intended for this area all along, and the two conduits leading away at angles toward the aft could be heading to each impluse engine?