Here's how I thought it worked out (and marked up below): Deck 1 Lower sat in the middle Deck 2, as if it's the donut hole to Deck 2 because it's a giant swappable module. The forward green stairs you have marked technically go from Deck 1 Lower to Deck 3. Similarly, the orange-arrow stairs (center-deck) start at Deck 1 Lower and go down to Deck 3. The Observation Lounge is Deck 1 (upper) and the red shaded area you marked is overhead crawlspace to Deck 1 Lower. The windows on the screencap are... discrepancies? Much like the lower saucer deflector.