Any idea why the Cooper S fuel cap is not chrome on the convertible like it is on the hatch or clubman?

Same reason it's not on the R52, there isn't enough space for the chrome one.

Something about the petrol filler and the motor workings of the convertible roof taking up too much space for the chrome one to fit in.

Funny I was at a show once parked next to Rakeys old amazing Chilli Red JCW MCS convertible done up to the 9s and this know it all woman walked past and said "thats not a Cooper S its not got the chrome petrol cap" doh! How stupid some people can be! I wanted to educate her in the world of MINI but I thought my efforts would be wasted.