Half the energy of antimatter annihilation is in the form of neutrinos,
I think you miss the crux of my argument:
In 1964-1969, there was no real explanation of precisely how the engines worked, nor how dilithium worked into that process. The engines were big, powerful, apparently worked by the controlled reaction of Matter/Antimatter, and needed dilithium crystals for the process to work. Neutrinos -- indeed, subatomic particles in general -- were never mentioned in TOS.
That's all we ever knew in TOS. Everything specific about how the engines work, the involvement of dilithium as a key factor in the M/Am reaction, etc ... all of that came about twenty years after
TOS had aired.
If you look at the Enterprise just as we saw her in TOS, there's no evidence that there is an intermix shaft (vertical, horizontal, diagonal, or otherwise) anywhere that we ever saw.
I contend that from the perspective of the ship as designed, the Engineering sets we saw were the engineering spaces that existed (though there's a hullfull of others we never had occasion to see). We never saw anything like a vertical or horizontal intermix chamber because Jeffries never imagined that one existed on his Enterprise
There was no M/Am reaction occurring inside the ship, but rather up in the nacelles. If there were an intermix shaft, it was located in the nacelles.
As an aviation engineer among other things, Jeffries understood that things that big and that dangerous simply shouldn't be handled by human beings in operational conditions. Running around a working M/Am reaction would have been something that almost never happened in Jeffries' world, and would have been dangerous as hell if it did.
I think to understand his perspective, you need to have been around when he was making engineering drawings. There was no microcircuitry: advanced computers meant lots of wires, resistors, capacitors, and plenty of Handwavium. Engines that drove big things were big: airliners, ocean liners, even the advanced nuclear vessels of the day had big engines.
Furthermore, the public love-affair with atomic fission was in its heydey. It's a testament to Jeffries' forethought that he understood that even fusion reactions wouldn't generate the power needed to warp space, so he went one step further with controlled annihilation reactions.
But he didn't get specific with it. It was big, it was powerful, it was inherently more dangerous than nuclear fission, and it needed dilithium (Handwavium) to work.
All the arguments about how the engines work that were developed in TNG and later do not retcon well to TOS because they are attempting to unify two radically different designs. I think it's fascinating to see attempts to retcon it, but in my opinion, it's still a retcon. It wasn't what Jeffries intended.
And that's fine -- the WWTD viewpoint is perfectly valid. I certainly find the entire exercise artistically amazing. Regardless of my feelings on the subject, this is one of the most creative attempts I've ever seen.