The size of the Enterprise was finalized in October 1964, and did not change after that.
I outlined the history of the only size change in my 2016 reconstruction of the original Enterprise plans...
And it is also covered in my history of the 33 inch model (
here).
On the question of why the diagrams weren't accurate to the 11 foot model... the first reasonably accurate plans of the 11 foot model didn't exist until the mid 1990s. It wasn't as if Jefferies could just scan the 11 foot model to make a 3D representation and use that to make illustrations for the show back in 1968.
And as for the readability of illustrations from "The Enterprise Incident", the episode aired on September 27, 1968... the same month that those same illustrations were published in TMoST. That was the 1960s equivalent to HD screen caps or other behind the scenes details published on the internet today.
Some interesting aspects of the models...
The bridge dome on the 11 foot model was originally oversized compared to the plans. The original bridge on the 33 inch model was correct. Jefferies stated that he had nothing to do with the window added to the 11 foot model's bridge dome, he wasn't consulted on any of the modifications to the 11 foot model for WNMHGB.
For the series modifications, Jefferies requested that the bridge domes be shortened to better match the actual bridge set. To make the bridge dome the height Jefferies' wanted would have required making a new dome for the 11 foot model because of the window added for WNMHGB. The cost was too much for Roddenberry, so the original dome was cut off just above the hole for the window... making it shorter than Jefferies had intended. But the bridge on the 33 inch model was shorten to the height Jefferies' wanted in the series modifications of that model.
Does any of this matter? No. You guys can make up anything you want as far as the size... but the history of the production of the show from some 60 years ago isn't going to change, and all those artists are now dead so there isn't any point arguing with them. They don't care what size you think the Enterprise is.
But please don't complain when the 1/350 model kit doesn't build a 4 foot model.