I would like to express the worry that we're giving a lot of weight to a number of crystals that is in fact established merely as a minimum
number in one episode, and basically contradicted in another. The fourth is the final in "Mudd's Women", yet loss of four in "Alternative Factor" leads to fewer problems than the ones experienced when the ship retained one half-working crystal plus battery power. And in "Elaan of Troyius", a single crystal saves the day by restoring full warp fighting trim to the ship.
I'd thus urge us to favor the interpretations where there can be as many as a dozen crystals aboard whenever Starfleet can afford them, but one is all that is truly needed. "Mudd's Women" would play out much the same if Kirk had sixteen crystals available but expended fifteen of them in the chase... Possibly full power calls for one healthy crystal in a key piece of machinery (a TNG style annihilation focus?), plus immediately available spares or the engineer won't risk the 100% setting. But whenever the ship has more crystals available, these need not sit idle, but can go to secondary applications where they do a lot of good (in addition to serving as main power backups if the engineer has the time and means to reroute power through alternate or bypass circuits).
By having the operational crystals always subjected to antimatter bombardment, TNG style, one would create a situation where a heavily shielded dumbwaiter system is required for all the applications. This system could then have multiple access points in multiple, nearly identical rooms, but with very specific single points of vulnerability wherever the crystals actually get utilized.
How much trouble would it be to pack four (or even six) of the later-season engineering rooms in the top levels of the secondary hull (always with two side by side and mirrored), assuming the forced-perspective set extension was taken to be no longer than it physically was on set, or possibly interpreted as somewhat shorter, even? The more, the merrier - and there could be several of the earlier, one-level-high rooms on the decks below.
On the other hand, these supposedly are
just control rooms. I agree that scattering just a few, asymmetrically at that, between massive pieces of machinery would make sense. And it might force the engineers to install snaking rather than straight lengthwise corridors in the secondary hull, to get past the machinery.