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.
Then again, if you need antimatter to load your torpedoes, then placing this application right next to all the other antimatter-consuming ones to create a "citadel" where you center all your armor and shielding is probably the way to go. Distributing these kaboom-prone systems all over your ships just means your ship will go kaboom all over!
Indeed, the neck would be smack in the middle of a bubble-type shield, and shadowed from enemy fire by both the major hulls even in purely physical (or skintight shielding) terms... Arguably the best protected part of the vessel overall.
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?
We never learned if this backstage speculation held true in the "real" Star Trek universe. In ENT, the similar-looking blue glowing thing is said to manipulate the warp field somehow, in comparable offscreen doubletalk by the creators of the design.
Perhaps both are true, and any energies pumped into this crystal will be used for adjusting the main warp field in such a way that it makes inertia do the crew's bidding? From the DS9 pilot we (canonically, for a change!) learn that manipulation of subspace fields is indeed important in facilitating sublight propulsion; perhaps starships with these blue crystal things manipulate their warp fields in order to adjust their inertial mass?
Does the fact that Khan's ship has two of these things and Kirk's just one contribute to Spock's assertion that Khan can outmaneuver Kirk?
Another thing to consider: Andy Probert placed Main Engineering in TMP directly below this crystal, allowing the vertical "core" (or whatever) to point straight at it. But the set was then boosted by a forced-perspective matte painting showing a long corridor towards the bow from Main Engineering, meaning the facility "actually" has to be farther back. Nothing wrong with that as such - but it means the upper part of the vertical "core" must either twist or terminate just a deck or two above Main Engineering. Perhaps it runs along the spine of the connecting neck and eventually reaches the crystal... Or perhaps it just hits a fuel tank inside the neck, like in the TNG design?