It was only in Franz Joseph's blueprints that the engine room was asserted to be in the primary hull. TOS was always consistent that Engineering was "the lower levels."
The Making of Star Trek also makes it clear that there are no engineering facilities on decks 7-8, only in the secondary hull. Doug Drexler's
Constitution-class
cutaway graphic from ENT: "In a Mirror, Darkly" confirms the position of Engineering in the secondary hull, directly under the nacelle pylons, with the triangular pipes being the bases of the power conduits extending into the pylons, and with the dilithium chambers on the engine room floor connecting to a horizontal intermix shaft running directly underneath it. (In my novel
Forgotten History, I chose to interpret the "nacelle interior" seen in "One of Our Planets is Missing" as actually being this intermix shaft.)
I've always hated that Franz Joseph completely missed the point of the forced-perspective tubes and depicted them on the blueprints as actually being short and tapering like the real structure on the set, rather than being the much longer, straight tunnel that the designers intended it to represent. It's weird that he replicated that so literally while also depicting the corridors outside the engine room in a configuration that contradicted the actual set.