Also, taking this all a step further (and i know we are side-tracking this post here), i think it's important to remember that Intel and Nvidia are competitors in the mobile market. It's seems unlikely that they would have any sort of special relationship in the computer market when they have already butted heads in the mobile market (and i believe i read that Intel was quoted as saying they are not in the business of helping their competitors over the last couple months)
From a business standpoint, it does not make sense for Either AMD or Nvidia GPUs to eliminate themselves from any customers by making their hardware perform better with either Intel or AMD cpus. They would want to be as competitive for the price as possible while maximizing their profits despite whatever other hardware exists in the machine.
Given all of that, i really don't see a logical reason that AMD would want themselves to be more competitive when paired with an AMD GPU, but i really don't see a legitimate reason to even consider that Nvidia and Intel would do so. really what you could say is that AMD has an opportunity to work better with AMD because they are the same company, and Nvidia/Intel has no such opportunity, or even incentive to do so.
Really, if you could test the actual performance of an AMD GPU with and AMD CPU against an AMD GPU with an Intel CPU that performs exactly the same (no such thing) as the AMD CPU, you would have some sort of idea about whether they work better together or not.