Are you, ever, in "can of worms" territory, with this one. The stark truth is that, probably, we'll never know. I have the 1942 & post-war Supermarine drawings, for internal finishes, and wheel wells are not mentioned, so you have to decide if they were considered as internal, or external, components. Apart from the cockpit, internal parts were silver, over a grey undercoat. The cockpit (and, at some stage, probably post-war, other internal parts) was grey-green over the same grey undercoat. If the wells were considered to be exterior, they would have been underside colour, over the undercoat. I've seen unrebuilt Spitfires, from the Mk.I to 22, with green wells, and just as many with u/s colour. One of the best pieces of advice, that I ever received, came from John Beaman, who said "Paint it what you think is right, and challenge the others to prove you wrong."
Edgar