I have a little issue with the idea of the warp core in the Constitution original and refit-classes taking up space in the "neck". It seems a bit careless to have something so important to have half of it in the exposed neck, close to the surface.
Then again, it seems careless to have the bridge be atop the primary hull, even though in-universe explanations about overshielding that area help explain it away.
And when they refit Enterprise and put twin torpedo launchers right next to the warp core, if it indeed goes up through the neck, well, that seems especially daft.
I tend to think of the Constitution (refit, at least) as having a warp core some 5 decks in height and entirely within the secondary hull. Such an arrangement would also fit in the Miranda-class without controversy and appeals to my sense of symmetry.
Regarding the "impulse engine deflection crystal", it's my understanding that it is meant to deflect energy from the warp core towards the impulse engines when needed, is that correct? And yet it seems strange that it's situated atop the primary hull when the warp core is at least a few decks down from it, or should be, to accommodate saucer separation. I could see the purpose of some kind of "deflection crystal" being a way to divert power from impulse engines to the phasers, perhaps (especially in separated flight mode), but not necessarily in relation to the warp core to the impulse engines.