At this point, we’ll probably never know for sure whether FJ knew of its existence [Auxiliary Control Room] or not?
What's the point in knowing? Either he didn't know of its existence or
he decided to ignore it.
In either case he wasn't qualified to be referred to as a Star Trek authority, mind a Star Trek expert.
One of the prerequisites to achieve such a status, IMHO, is substantial knowledge of the matter to some extent and
its accurate, unbiased reproduction (which doesn't exclude different interpretations on why and how a certain component does function). YMMV, of course.