Just looking at the Hasesgawa models, Shin's VF-0A(the one with the Ghost) looks pretty generic, like a cannon fodder. The graphic is minimal and color is generic 2-tone sea grey. I think it was just a replacement pane they had around...a spare. Also figuring he was paired up originally w/ a copilot(avionics), they put him in a 2 seater, hence the VF-0D.
Just my 2 cents...