The problem I have with that idea is that no material, by virtue of pure physics, can "store" that much energy.
Most of those lines work adequately in the sense that you define them... but most of them also work in other forms as well.
Let's just be clear... I know we all get this, but for the record... different writers had different ideas about how the Enterprise worked. These ideas are, in some cases, inherently contradictory. While your efforts are a good attempt to make it all fit, there's nothing that can make EVERYTHING fit. We have to "pick and choose" one way or the other...
Your points about the crystals "storing power" aren't really any more relevant than the idea that crystals "transform" power. In both case, the crystals are a "source of useable energy." It's just that in one case you have them "transforming and storing" while in the other case you have them merely "transforming" (and the BATTERIES are what store power).
I think "That Which Survives" is one of the absolute worst episodes of Trek, along with "The Alternative Factor" and a few others. And I'll admit that my taste for the technical stuff created by a writer is much greater when the writer wrote a story which didn't make me want to gag. But that's purely a personal perspective.
Still, there's nothing in TWS which requires there to be a single central reactor. Nothing at all. All we know is that there seems to be a single CONTROL MECHANISM. Nothing... nothing whatsoever... tells us that this control mechanism is physically attached to the reactor core(s).
People usually hear the term "antimatter integrator" and assume that this is a physical, mechanical element of the reactor core. But there is no reason to conclude that. There are elements of modern nuclear reactors which have similar nomenclature which can be miles away from the actual physical reactor cores, after all. The "reaction initiator system" in a modern reactor is basically a big hydraulic system which retracts the neutron-absorbing rods from in between the fuel rods, after all. So when I saw that episode, what I saw was the equivalent of that sort of a system.
Doesn't prove I'm right... but it'll be damned hard to prove I'm wrong, either, won't it??
FYI, you do make one judgement which is ENTIRELY unsupported and unsupportable. You concluded that, because a shuttlecraft explosion would leave antimatter residue, this means that the shuttlecraft is "warp powered."
Well, I do agree that shuttles have FTL capability (not necessarily "warp drive"... unlike most others, I do not treat "warp drive" and "faster than light drive" as synonyms, but rather warp drive is only one of many forms of faster-than-light propulsion). But the presence of antimatter only infers the presence of antimatter, and LIKELY of a matter/antimatter reactor.
So... if a planet has matter/antimatter reactors for planetary power, does that mean that this planet is warp-powered? I don't think so, do you?
The one thing we can take from this line is that the shuttle has antimatter aboard, likely for use in power generation (though it could be from something else as far as we know!)
The line about "reactors 1, 2 and 3" makes it clear that there are multiple reactors aboard, true... but the line wasn't "antimatter reactors 1, 2, and 3," was it?
For that matter, the idea that there are "single reactors" is not necessary supported, even in the models we've discussed. For instance, in my warp drive nacelle layout, there are four rows of reactor cylinders in each nacelle... so there are, by at least one measure, a couple of hundred "matter/antimatter reactors" (though I treat each as a subsystem, and call the whole assembly in each nacelle a single "reactor assembly").
To take this to the other side... the one I don't personally buy, mind you.. suppose that the "cathedral of tubes" is actually the reactor assembly. There are what, six rows of tube-triangles, right? Maybe this means "devote half of the output of this main reactor assembly" to the purpose you mention (leaving the remaining three reactors to their primary purposes)?
It's a mistake to assume that just because TNG has a single reactor, other ship layouts are set up that same way.
Perhaps, in TMP, each "segment" of the core we see is an individual reactor?
There are still far too many undefined variables to come to a single, unimpeachable conclusion, I'm afraid. But I do admire you for trying so hard to make everything fit... tilting at windmills, so to speak.
For me, I have my own "model" for the ship in my mind and the bits that don't match up exactly (from Elaan of Troius, mainly...) sort of get a "mental retcon."
Very little "doesn't match up" though... since I view the crystals as what turns UNUSABLE matter/antimatter reactor output into USEABLE energy. Most of EOT works just fine, with just two lines requiring a minor tweaking.
And if someone else has a totally different idea... say, a single centralized reactor... that's OK (even if I'll NEVER agree with it!). They have to reject some things, just like anyone else does. They're just rejecting bits I, personally, want to keep, and keeping bits I, personally, am more than happy to reject.