The flight deck isn't showing rust.
I don't know why, but for a time, the US Navy finished CV flight decks with a light tan to yellow no-skid. The landing area was dark, the rest of the deck was light. I've seen photos of the Ranger and the America with decks in such a configuration.
The reason for the different colors in the photo and therefore the model, aren't clear. I imagine some of the deck was getting fresh no-skid prior to trials. Other parts were still covered with the lasting effects of yard grime; from testing, office trailers, etc., being on the deck.
As to the non yellow deck stripes, that comes from using some Italeri decals. Their "yellows" are too orange. I wasn't keen on painting the stripes, so I used some spares I had. The deck colors are a guess. The original '61 photos were color slides heavily shifted magenta from age. I did some digital color correction and then did a "best guess."