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This is Engineering?

One could also postulate that the "warp core" of the TOS movie ships was located underfloor at the bottom of the vertical "plasma conduit" shaft seen in the first movie, was at most three decks high and possibly just two, and basically always sat in that TNG style facility. It might have looked a bit different in E-nil-refit than in E-A aesthetically, but functionally it could always have been hiding in the lower forward part of the secondary hull. After all, we never saw the forward bulkhead of the cargo hold, and can push that aft quite a bit to accommodate such a warp core facility.

The other option is to have the E-A core replace the E-nil vertical conduit wholesale, as shown - and placing it aft and the turboshaft forward is what works better for the E-nil as well!

Why no space for tankage? A sizeable part of the connecting neck is porthole-free and might be a tank, not much smaller in relative terms than the E-D one. And there's always room at the bottom...

Timo Saloniemi
 
Why no space for tankage? A sizeable part of the connecting neck is porthole-free and might be a tank, not much smaller in relative terms than the E-D one.
The dorsal support pylon would mostly consist of walls and support structures, so I'm not sure how much deuterium you'd actually fit in there.

And there's always room at the bottom...
Except that (according to the above cutaway) the bottom deck is already full of corridors (and probably the Brig as well) and in any case, the "core" conduit runs all the way to the bottom of the ship.

I do take your point about the conduit only needing to be 3 decks tall (unlike TMP where we actually saw it running down 5 or 6 levels to whatever was at the bottom). So, with that in mind there could be plenty of space for fuel tankage and even a large M/AM reactor, ala TMP. The repurposed TNG dilithium core itself then would be nothing more than a large junction box, with plasma conduits running off to the various power and engine systems.

But if the reactor is below (with its extra thick power shaft running up and into the junction box) then why is there an extra one coming from above as well? I like the layout of the above cutaway with it's third plasma conduit, but if the M/AM reactor is below, that means there is a also 4th conduit as well! where would it go? And why is it so thick?
 
The dorsal support pylon would mostly consist of walls and support structures, so I'm not sure how much deuterium you'd actually fit in there.

There's very little evidence of internal bracing elsewhere in the ship, so the skin might well be the load-bearing structure here. And it's not as if there's all that lot of gas in any of the starship designs that explicitly (well, backstage-explicitly) do use gas tanks.

But if the reactor is below (with its extra thick power shaft running up and into the junction box) then why is there an extra one coming from above as well?

The extra thick thing wouldn't be a power shaft at all, but part of the reactor. Fuel and anti-fuel would come through those thick parts, TNG style, react at the middle to generate power, and the power would then go out through those two (three? just one? ST6 is ambiguous there) horizontal thin shafts. One would then angle sharply up and protrude through the area shown in TMP and ST2 where it would further branch to the nacelles and the primary hull.

Archer's core might be the same thing on the side and without transparent bits, because the tech needs lots of physical armoring at that point. TOS still leaves the core belowdecks and opaque and armored, be it vertical or horizontal or spherical or whatever; TOS movies peel off some of the armor as forcefields handle the job better; and TNG tech finally allows everybody to watch the light show at close range in shirtsleeves... But the plasma conduits stay the same all along.

Timo Saloniemi
 
So, the TNG warp-core is just a subsystem in the overall TMP style engineering setup? That does tend to diminish its importance somewhat, but I suppose it could work.

As regards to how many of those plasma conduits we see attached to the core, thanks to some clever camera work we only ever get to see one, so there can be as many (or as few) as you like! I suppose if there were just one then the room would have to be oriented more like a diamond than a square, but that's not the end of the world.
 
Or then the setup is not symmetric along the axis of the ship, which ties in with the well-established fact that starships only have a starboard power coupling.

Timo Saloniemi
 
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