I believe that their dyno does provide some ram-air effect. Although, there have been some questions raised about how effective it is. Regardless, the ram-air effect would be the same for all of the bikes. The only question is whether or not the bikes are level, i.e. all blueprinted samples provided by the manufacturers (probably) or a mix of dealer stock and manufacturer sourced.
I think that these engines are close to what is possible with current technology given reliability versus max power constraints. For example, the R1 has a lower compreession ratio than the ZX-10R. Therefore, other things being equal, it will produce less power, but will be more reliable. Regardless, and perhaps more importantly, the current Superstock rules allow the substition of the stock gaskets with thinner versions; thereby, increasing the compression ratio and commensurate power.
Okay! The above is my rationalization as to why it is OK with me that the Kawi produces more power (if in fact it does). Apparently, when MCN tested the bikes, the R1 was more powerful than the ZX-10R. However, I am not sure that their dyno provided ram-air which might account for the discrepancy since the Kawi's ram-air is probably more effective than the R1's (higher pressure location, etc.).