Personally I think WSBK should be a purely production based series with few if any modifications allowed to the bikes, run on production based tires you can buy at your local bike shop..
I think you are confusing "production" and "stock". Production bikes are whatever people are willing to sell on the open market. Stock bikes are street-legal machines built for mass consumption. Mixing stock bikes and production race bikes has never worked terribly well, unless it's a feeder class. Production race bikes should probably always be based on stock machines. Prototype should include equipment, built to formula guidelines, that the manufacturers would never sell or lease on the open market.
I also think SBK and GP are too close in performance. If GP was still 2t, I wouldn't care, but they are slowly becoming clones. I also agree with Domenicali that the Aprilia CRT is against the spirit of the regulations, but I think it is within the vision of Dorna/Bridgepoint. The claiming rules were intended to discourage factories from getting involved b/c they don't want their SBK parts claimed by other manufacturers. The bigger vision of Dorna, imo, is for GP to own 1000cc and the related production bikes. Not sure what will happen with SBK, but we know the MSMA don't like the 1000cc base anymore. Not sure why Domenicali would complain. Just claim the bike, and release the parts specifications on the internet so anyone can build Aprilia WSBK parts.