Some well thought out reasoning here, on everyone's part, for actual power generation happening in the nacelles.
I don't think it was ever more than an assumption that the M/AM intermix chamber was below the deck/floor in the TOS engineering section, based on the location of the dilithium crystal receptacles in the assembly mounted in the middle of the room.
I'd always assumed those rows of canted risers in the cage at the back of the TOS engineering section were feeding plasma to the nacelles, but the opposite might make even more sense. They cant in at the top, not out towards where you'd expect the nacelles to be in relation to that area, though by many depictions the risers would be sitting in the shuttlebay if they were lined up with the nacelle pylons anyway. The inward cant might indicate a more convoluted heat/energy exchanger system for plasma coming down from the nacelles to supply power to the rest of the ship, instead of the more direct route that would be expected for high energy plasma on its way to the engines.
It seems that things got further away from Matt Jeffries' functional simplicity over the years as more "chefs got in the kitchen" and decided what made a cool looking set instead of workable ship layout.