In what way is Andrew Probert not an authority on what is what, on the Enterprise-D?
In the way that the Enterprise-D is not real, Andrew Probert didn't design a spaceship, he designed the shape of a thing that everyone pretends is a spaceship. His intentions of what is what are just that, intentions. He intended the saucer rim to be one deck for example but we all know that the show made it two decks, what ends up on screen counts, everything else does not.
What he intended to be windows was never identified as such on the show, that means it's just an unidentified glowy thing on the saucer, there's no proof that it's not a warp drive.