It's good you have a pro to build the coop. He'll probably have that coop together quick. It took me (Not a pro,but I like the work) a coupla months to get mine together. I pre-built the wall sections in my garage, then dragged everything down and put it together like a 3-dimensional puzzle. I see what you are saying about space filling material, with the windows. It'll make it easier to peek in there and see what's going on.
About the 2X4s. Back in the day when they said 2X4, they meant it. The board was a full 2X4", not 1 1/2 X 3 1/2". It was a lot stronger board than what we get today. Also, that's another reason for the sharp roof pitch on the deeper part of the coop, to shed snow. They had this all figured out, as they got mass amounts of snow back then too.
Now as far as nest box placement, mine is straight across from the entrance door, inside the coop. You could, if you want, hang them off the side externally. But I've read about folks having a problem with frozen eggs with external boxes.