Regarding the shuttlebay size:
You have to keep the size of the doors in mind. From the outside, there are 4 left and 4 right segments, the outermost ones not as wide as the other. From the inside, we see 3 left and 3 right segments and their curvature suggests that they meet not so high above the semicircular rim with the two small observation rooms on them. So the doors couldn't be so much larger than the shuttlebay interior as your example suggests.
An outside view:
An inside view (I think it is the original model):
Regarding the "windows":
Yeah, they could
be something else than windows. But then the "windows" on all later ships also have to be something else. I think that goes a bit to far. But I like the idea that the smaller, round ones are sensor windows.