I never meant to say that the TOS sets could be smaller than what we saw onscreen, only that the sets we saw in TOS needn't be the only representatives of room height. Some areas might be 10' or 12' high, and Jefferies allows for that. Other areas will need to be 7-8' high, and he indicates that as well. (Our earlier discussion was about Ariel and was based on the TMP sets, which are an entirely different story.)
As for "windows" indicating deck position, who says? The times we see "windows" in TOS-- in Pike's cabin and in the gallery above the hangar deck -- they are a hell of a lot smaller than those "windows" on the exterior. It is arguable from that onscreen evidence that the windows aren't windows at all, and that they are "environmental sensors" capable of showing the view from any of those rectangular imagers (just as Franz Joseph claimed they were). If the huge outside rectangles and circles aren't inextricably linked to the small windows with the rounded corners on the inside, there is absolutely no evidence of where the decks are located. Which is as it should be because the windows were fudged on the model after the scale of the ship was changed, and in no way link up with the deck placement the designer -- and presumably his bosses -- intended.
Don't get me wrong, I enjoy your own drawing of the Enterprise "guts," though I find the extensive terraced "stair-stepping" and the huge variety of different craft stuffed in there to be far too different than what was seen on-screen for me to "accept" it as the "correct" presentation. That's the fun thing... trying to make everything fit in a way which works with the image each of us carries around in our head, isn't it?
When I did that cross section I was trying to see whether Jefferies' own cross section could be reconciled with what we saw. If you follow the route I've outlined-- going with a hangar adjusted for distortion, putting the sets where his deck heights allow them to fit, etc -- it works. Even the number of decks in the saucer fits if you count every level I've indicated as a deck. And those oddball support craft seen in the hangar and maintenance areas below? All of them but one were designed by Jefferies (only the repair capsule wasn't). Again, I was testing him, and when you lay out the decks as he indicated and scale his support craft in a sensible way, they fit.