^Back in the day, I used to think that those windows were where the Red Dec were (until TVH I did not know that they were on the same side). Now that I think about it, I kind of wish that they were. Simply because it would be nice to tie an element of visual interest on the model to a part of the ship we saw. In TMP, the closest thing would be the Rec Deck. We see it a couple times in the film (even though it was only seen in that one film, the model WAS made for TMP. The other films were just gravy). Though I realize this doesn't make sense as far as the deck layout is concerned. TWOK was the first time we had an interior for some "distinctive" part of the ship (aside from the bridge).
In a similar vein, I wondered what was behind that strip of yellow windows / lights on the Enterprise D neck.