Chili is on the Ducati website as having a 998RS03, which I suspect is a 998F02 - the same bike Bayliss didn't win the championship on.
Usually the previous year's factory bike (the F bit) becomes the customer spec bike (the RS one) for that season.
So this year's 999RS04 would have been last year's 999F03 - Hodgson's bike.
Ducati won't give the same bikes/engines to it's customers as it has for the factory team - same in MotoGP.
Besides, the engine from the 998F02/998RS03 would indeed be the same 999cc engine from the 999 range, just without the go-faster improvement the factory have made.
As for tyres - it doesn't really matter as Chili made an excellent, experienced choice to run the tyre he did and it worked out right for him in the end.
It's his local track and you can't help feeling that he knew what the weather would do and made his tyre choice accordingly.
Probably!
