This is why there will never be deck plans of the new Enterprise. If the size is 725 meters but the ships windows and doors show it to be half that size, how do you make a blueprint? Since the ship was rescaled to make the hanger deck look large enough, it now doesn't work. If you look at a side view of the ship, the shuttle bay door looks to be no more than 25 feet tall when comparing it to the docking port door on the side which is probably no more than 8 feet tall. To cram 2 shuttles on two seperate levels and leave enough clearances for entry and egress, you'd need a bay closer to 40 feet tall.
If you tried to blueprint the ship as is, and scale the decks off of the bridge, what you end up with is a shuttle bay thats only about two decks high. So unless their running micro shuttles and only carrying children, it will never work on paper.
Wrong. See HERE
for how it all fits together, bridge, windows, shuttlebay and all.