Here's a comparison shot from "Where no one has gone before" that shows how the 2-foot model, which didn't have interior window lights, finally got those lights for the remastered version of the episode. Isn't that just excellent?
They added them to the warp-away in the title sequence too.
I wonder how they did it? If it's not a CGI recreation, that's a lot of little lights to track frame-by-frame!