That was my logic. You get x # of cc's. Lets see what you can do with it. It seems strange that they make special rules for Ducati. But it's not my business, so what do I know.
What most people don't realize is that Ducati has not been playing on an even playing field with the in line 4s for almost 10 years. To keep competitive, most WSBK and AMA bikes are nothing like the bike you can buy from your "local" (as most of us know there are very few that can claim they have a local Duc dealer) dealer. Think about it, since the 916 and early 996's, how many privateers have ridden and placed in the top 10? Now, look back at the number of privateers on an inline. The key here is that the twins have fallen behind year after year, and the only thing that keeps them even somewhat competitive is more money thrown at the engine in the form of light weight unobtainium and other such things not available to those with normal bank accounts. Could Ducati have stayed competitive without the displacement advantage? Sure, but their argument was that it was not cost effective to do so...and can you blame them? Now that the cc limit for a twin has been bumped, I believe the amount of other concessions that they were allowed has been dropped. Think about this, if you can take a GSXR 1k off the showroom floor, rework the suspension, slap an exhaust on, and remap the ecu vs. buying a 999, reworking the suspension, tear down the engine, add high comp lightweight pistons, lightweight crank, light valves, different cams...etc, slap on an exhaust, remap. Which would you do? Keep in mind the 999 already costs almost $10k more than the GSXR to begin with.
In a perfect world, a twin and an inline, or even a V4 would make comparable power without the need to do major work to make one as competitive as the other. But this is not the case unfortunately. Not that I like Nascar, but they too deal with short comings of one manufacturer compared to another. Not only do they restrict engine size, but they also make sure every car body fits a template. They do it to keep everyone in the same ball park....which is why Ducati (being the only twin still competing) such a large displacement advantage. Now if Ducati starts running away with everything, I am sure the sanctioning bodies will impose either a weight penalty or possibly rethink the displacement rule mid season. Everything has a way of equaling itself out. And by the time the rules get changed again, if the twins are at that much of an advantage, the in-lines will have improved to match them, and the cycle will continue as it always has.