So Im right in assuming that we can accept Franz Josephs warp nacelle configuration? The struts would have no connection to the tube room?
For the TOS era designs, yeah, I'd say that is pretty correct.
I've always assumed that we weren't necessarily seeing every piece of functional equipment. I think of the "rows of tubes" as being the ENERGIZER... the part that converts the raw radiation from the m/am reaction into usable energy (electricity, really) for powering shipboard systems. In front of the energizer is the main engineering complex... and BEHIND it (ie, at the far end of the rows of tubes) is where the main reactor hardware is located.
It's alternatively another position I consider that the tubes make up a bit "parallel" reactor assembly, with multiple smaller reactors in three parallel sets of ... what, 12?... SERIALLY arranged reactors.
But while I sometimes consider that, I usually end up going back to the idea that theres a reactor "hidden" at the far end of the "tubes" room.