I don't think we can ever properly compare the two consoles, or for that matter, ps3 vs 360 vs wintel vs gpu. As the ars technica article and the folding@home pages themselves state, the folding@home client is specifically programmed to maximize the strengths of the different processors, because they are all good for "something".
I think the analogy used in the ars technica article explains it quite well, really. If we were really to compare them, we would have to run the same tests for all cpus/gpus and it would be no surprise to see areas where one processor smokes the other, and vice-versa. But what's the point in speculating if this will never happen? Even if the 360 gets around to folding, it would most likely be running software optimized for its processors, and chances are they will be different from that of the PS3. So in the end, the comparison would not be valid anyhow, and I doubt Stanford would go out of their way to create benchmarking software to pit the two consoles against each other - they are more busy trying to, you know, cure incurable diseases and all that. They have better things to do with their time!
Finally, what's the point of having one console fold better than the other? I want my console for games!