I have to say that I'm loving this thread so much. I will put in my two cents though. With regards to sizing, I think there is some ambiguity on scaling, but that's just modelling as far as I'm concerned. But things like window placements, and for things that appear to be windows, especially from TOS to the movies and TNG, I'm pretty sure no one made designed these models thinking "let's make things LOOK like windows BUT they aren't... heh heh heh... We'll confuse the heck out of everyone!"
I know my example is a little facetious, but I think my point is made. Sometimes a cigar is just a cigar. It's nice to try to pigeon hole our own preconceived and contemporary notions into things like is it a window on the dorsal or a scanner, but I think we're over analyzing in that case. Sometimes a window is just a window. I really don't think there was any hidden meaning behind the dorsal windows, or big 3 bow windows (we'd all like them to be scanners of some sort), or top of the bridge.
Gotta go to work now. Miserable day for a commute.