I do however, think some small allowance can be made for the fact that a civilization that can build such a ship, and bend space and time, can finesse the problem of waste heat.
Still, I'd rather see science fiction that actually acknowledges physics and designs the tech with it in mind, rather than just doing fanciful stuff and saying "Don't worry, a science wizard did it." That's what made Jefferies's designs so great -- they looked practical and plausible.
Besides, as they talk about on Atomic Rockets, waste heat is not a casual problem to "finesse." Even the most advanced technology can't ignore the laws of physics, but must work within their limits. And the laws of thermodynamics are pretty non-negotiable. Sooner or later, energy will end up as heat and that heat has to be dealt with. That's something even super-advanced technologies can't ignore. (In Niven's Known Space, as revealed in the more recent novels he co-wrote with Edward M. Lerner, the reason the Pierson's puppeteers' home planets don't have a star is because they're so heavily populated and urbanized that their own waste heat keeps them livable and they need to be in deep space away from stars to keep from overheating. That's an incredibly advanced technology, but it's still bound by thermodynamics.)
But I do think a proper understanding of Jefferies’ intent would have huge M/AM reactors and fuel stores in the nacelles, but also some kind of reactor and fuel stores in hull.
"In hull" is one thing, but right in the middle of an occupied room is another. It would be more plausible if it were in a separate compartment shielded off from the pressurized, inhabited sections of the ship.
After all, Trek-universe engines are disturbingly prone to explosions. So it seems like a good idea to keep them in separate compartments that are easy to jettison. And that's another advantage of keeping vacuum between them and the crew, because atmosphere propagates and amplifies blast effects enormously. A nuclear or antimatter explosion in atmosphere causes immensely more damage than one in vacuum, due to the superheating and expansion of the atmosphere itself.
I mean, really, there's no reason why
every interior volume in a spacecraft needs to be pressurized. In
Gene Roddenberry's Andromeda, which in its early seasons (before staff changes and retools dumbed it down) was the hardest hard-SF show prior to
The Expanse, it was a standard battle tactic to vent atmosphere from most of the ship's volume so that there wouldn't be any blast effects from relativistic projectiles penetrating the hull (since they had no shields).
The only indication in my mind that Jefferies originally intended the main engineering set to be in the saucer in fact deals with Christopher’s objection- not only does his set have a curved corridor outside it, but the impulse engine is where he put some kind of radiator on top.
Well, the engineering set was at one end of a short straight corridor that ran perpendicular to the curved corridor. Whether its connection to a curved corridor is visible depends on how the director sets up the shots. So it could've been that the intent was that it was in the secondary hull, but not all directors bothered to keep that in mind. Sort of like how you could sometimes see the edge of Spock's station even though it was supposed to be flush with the adjacent station. Or how some TNG and DS9 directors didn't bother to hide the fact that there was a flat forced-perspective painting on the wall behind the actors rather than an actual corridor or Jefferies tube segment. There's a difference between what the camerawork betrays about the real-life set design and what it's meant to represent within the fiction.
Anyway, forced perspective is why I don't buy Franz Joseph's placement of the engine room in the saucer -- because the "pipe cathedral" section was clearly meant to be a forced-perspective piece representing a longer tunnel with parallel edges (like the TMP horizontal shaft), but FJ took it literally as a short tapering section, wasting the whole illusion. I'm fairly certain the intention was that the "cathedral" was supposed to be a glimpse back along the length of the secondary hull.
I suspect it may gave been intended to be an ambiguous, duplicated space that could fill in for impulse and warp engineering.
That's a possibility, though it's hard to reconcile with my take on the "cathedral." But in the first season, they did go through a variety of different configurations of the set, and you couldn't always get a clear sense of its overall layout.
Still, they did generally refer to engineering as "the lower levels" or the like.
