The confusion goes back to how tech issues were handled back during TOS' production. The Writer's Guide (from which most of the tech info for "The Making of Star Trek" is derived) is very vague on the matter. The series itself was all over the map, generally depending on the nature of the episode and the crisis being presented.
It breaks down thusly:
If the situation amounts to "the ship is going to blow up unless such-and-such happens on the planet" then the writers tended to be very vague and go with some general reference to the nacelles. The solution to the problem had nothing to do with the ship itself, so no real thought was put into just what exactly was going wrong to endanger the ship. Blow up Landru/Vaal/whatever, and the systems will magically reset themselves.
If, however, the solution relied on Scotty actually fixing the problem in order to save the ship, it's amazing how detailed things get regarding how the ship actually works.
In "The Naked Time" we learn about the mixing of matter and antimatter in order to generate power for the ship. It's also where we first hear the term "intermix chamber."
In "Mudd's Women", we learn about the role the crystals play, in channeling the ship's power and make it usable.
In "That Which Survives" we have direct reference to the Matter/Antmatter Reaction Chamber, abbreviated in the TNG Tech Manual as M/ARC, and often referred to as the "warp core." We also learn that it's one unit, probably somewhere in the secondary hull near Engineering, is not meant to be manually inspected while the unit is in operation, and can be ejected.
In "Elaan of Troyius" we have a much clearer depiction of the dilithium crystals, what they do, particularly when they have to replace the burned out crystal with the rough stones of Elaan's necklace.
These instances laid the groundwork for the layouts we've seen ever since TMP, and most clearly depicted from TNG onward.