There is no requirement for positioning the vertical shaft at any specific point on the central axis of the ship, no. Its upward reach is not seen, beyond the two decks' worth that exist on the set. Its downward observable reach is comparable, or a deck greater, in a single ST:TMP shot that appears to involve forced perspective and some mirrors.
Beyond that, the shaft could make sharp kinks, or split, or truncate in fuel tanks, or whatever.
I don't think it a big problem to fit the shaft next to the ST2:TWoK torpedo deck, really. Indeed, if the shaft carries antimatter, then it would be nice to have it close to the torpedo loader that supposedly injects antimatter to the warheads just prior to firing.
OTOH, I do think that moving the entire Main Engineering set farther aft than Probert originally intended would be a good move. It would make possible and plausible the long corridor observed extending dead ahead of Main Engineering in ST:TMP, for one thing; this corridor would then truncate in the master vertical turbolift shaft between the two hulls - the feature that is flanked by the greenish "armor panels" on the outside of the model (where Probert expected the vertical shaft to be). The repositioned shaft would then probably truncate in a fuel tank within the neck, much as in TNG-era starships.
Something like this, modified from Shane Johnson's cutaway in Mr Scott's Guide
Perhaps combined with this sort of a torp deck layout:
While I like the idea of moving Main Engineering back some, and perhaps bending the shaft to run parallel to the Jeffries Tube to the IDC, and I like that Torpedo Deck layout much better, that winds up placing the bottom end in the Botanical Garden (Is it sufficiently shown on screen that the row of blue windows is in fact the Botanical Garden?) which again runs afoul of practicalities. Could those windows be explained as part of the antimatter containment instead? IIRC, we see some vague shapes inside that imply (but do not actually establish) trees or bushes. If it was a more uniform blue, I might much more be willing to accept it as antimatter storage.
I guess that begs the question: Why would you want large windows like that on the Botanical Garden (if that is what it is)? You aren't going to get sunlight for the garden that way, you are going to have to artificially create the illumination for photosynthesis anyway. For the crew to look out? There are windows all over the ship. These windows are HUGE - a significant vulnerability for a ship that could be in combat.