I don't see how that article is related, really. The cracking on paid links issue has been known for a while, and essentially means you may consider putting a nofollow tag on anything that isn't a hard-link exchange. It makes no difference whether these are links to sponsors, to toplists or anything else. And it doesn't mean that the affiliate links with ref code somehow boost the overall PR of the root of a domain.
BTW, I think Matt Cutts explained in the original blog post he made that buyers won't be penalized, only sellers (or perceived sellers).
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