But back on point: on this issue FJ deliberately ignored a well established fact of the ship as seen onscreen. I'm not giving him a pass on this one.
In assuming he deliberately ignored the Auxilary Control Room, you presuppose that FJ had seen and noticed it in the first place.
After having read the interviews again at www.trekplace.com
(which is an excercise I can't repeat recommending) there is no substantial hint he was aware of these and other interior compartments not
featured in the studio set blueprint of The Making of Star Trek
or in the film stills accessible to him.
You can read in these interviews how uncomfortable he was going to Star Trek Conventions and how he emphasized that his work should not
be considered to be a bible of some kind (someone should forward these interviews to James Dixon and friends).
It shouldn't take a lot of imagination that during those conventions he meet Trekkers that did ask him those hard questions like "Where's the Auxilary Control Room". What was he supposed to say?
"Sorry, I based my work entirely on the information I got from The Making of Star Trek,
a couple of film stills and an occasional item here and there I noticed while watching the reruns with my daughter"?
Fans looked up to him like a guru, almost a Carlos Castaneda thing, and he didn't have the heart to tell them that he was not the kind of Star Trek expert fans assumed him to be. IMHO, he made that clear in the interviews. Apparently he enjoyed his status as a guru because it enabled him to promote his ideas of space exploration and political participation.
I can't, won't and don't blame him for that.
Therefore, I believe that by emancipating ourselves from his work and using our own knowledge to come up with a different kind of technical manual would rather be something he would have approved and encouraged. Didn't somebody mention IDIC in the course of this thread?