This was always a problem. On the top of the saucer, allegedly, was Captain Picard's quarters, where you see these windows, and the set windows are not LONG enough.
It would have been good if there was somewhere on the sets that had the lower windows like that. It almost was, in "First Contact" movie, where Picard was showing the Earth, out of one of the windows, which was sort of like a lower window like that.
But, this is sort of like the "Jupiter 2" saucer from "Lost in Space", the model doesn't fit with the set design.