ITRW, a major vertical piece of machinery is a good way to rationalize (and dramatically utilize) the otherwise insane-looking neck section of the hero starship. It would seem Andrew Probert went for the "utilization" angle in ST:TMP and finally also for the "rationalization" angle in TNG, after which Sternbach and Okuda did their best to carry on the tradition with ships of different shapes (including the oddball Oberth
In-universe, I guess any orientation will do, but the currently postulated nature of the thing as a linear accelerator between two tanks probably does dictate a thing or two. Especially when one of the tanks needs to be ejectable in a hurry, even if the core itself perhaps need not be.
should not be retroactively used
Why not? We retroactively use "Starfleet" and "Federation" for Kirk's bosses even for the earliest TOS episodes.
Although I personally think we never saw a matter-antimatter reactor in ST:TMP, merely plasma conduits going this way and that (because from TNG we know that this is exactly what a plasma conduit looks like). The actual reactor in both TMP and TOS might have been buried somewhere in the lower decks, heavily shielded.