Well, Franz Joseph made up some things (his flag designs were so good, some were later screen-used). But he followed The Making of Star Trek (1968) for every decision that the text would touch upon. He devoured that book.
One example is on page 171 (first page of Chapter 2), which says that headquarters for the engineering division, plus main engineering control facilities, are located at the aft end of the primary hull, by the impulse engines. This page also mentions that the saucer is eleven decks thick through the middle, which FJ followed.
The book was at least canon-adjacent, coming straight from the source. But I do see this mismatch between it and the arched "ceiling" of the Engine Room set.