The premise of the article is that you happen to stumble upon a messy piece of code and that the explanations related to it might be located into the source history. Yet the only reason why these explanations would actually be there is that someone would have enforced doing that as a rule. And the point of the counter-argument is that before enforcing this rule this same person should be enforcing a rule saying that writing messy code like that is prohibited.

In short, maintaining a clean code base has always higher priority than maintaining a clean log.