See, that was why I would never have considered that illustration as a primary source (that, and the fact that there isn't a way to make accurate scales for it). That is why I had dismissed it for nearly 40 years.
No, instead I used the Phase II cross-section as my primary source for deck heights, and then use the writer's guide illustration to corroborate that information. What struck me as so odd was that if there wasn't any real fixed information on the deck heights of the Enterprise, and the Joseph plans were the ones all the fans were using, then why are the heights between a small drawing for the writers in the 60s matching up with highly detailed drawings of the Phase II Enterprise in 1977?
What I was forced to conclude was that while the writer's guide drawing may not be the best source for this information, it does confirm that Jefferies had worked it out by the time that he drew that picture and that he stuck with those deck height specifications for more than 10 years and even at a time when he was willing to make other alterations to the Enterprise (like the diameter of the primary hull).
It seems to me that the deck heights of the Phase II plans working with the set heights of TOS and lining up quite nicely with a non-detailed drawing for some writers is beyond coincidence.