The top/second level is probably for the primary flight control (pri-fly) -- note that the second level extends out more in the port direction over the flight deck, and has a perspective to the rear of the ship as well, i.e.: the second level has a field of view that can surveil the overall flight deck to the front, port and rear side relative to the island.
The bottom/first level is probably the bridge, for navigation of the ship itself -- the first level only has a perspective to the front of the ship, with partial views to the starboard and port directions.
On the Nimitz class, the pri-fly is on the highest level, and you can see that the windows are similarly only on one half of the island, whereas the lower two levels of the island face forwards fully. The pri-fly level also has windows that are a bit larger.
The Ford shows it even more obviously.
From the front you can see that only the second level from the top has windows facing forwards the full width of the island, is the navigation bridge.
However you can see multiple other levels where the windows only are on the port half of the island, and from the rear perspective you can see how the levels have a rear view of the flight deck.
I don't know which levels on Ford are its pri-fly, but I bet it would be the topmost one given the marginally greater size of its windows. That combined forward and rear perspective are sufficient for primary flight control purposes of the flight deck.
.... so the answer as to why the windows on the top level/pri-fly level don't extend the full width of the island, I suspect it's because they don't need it to extend the full width -- extending it the full width wouldn't provide any additional field of view for flight deck control purposes.
