He denies that he created the idea, but he has spoken about it ("making an X on a calendar"). In his mind it probably seemed like a simple observation (he's pretty good at those), and I could imagine he was surprised people took it to a near-religion ("the Seinfeld productivity program").

I'm not sure it's accurate to say he denies "that he ever had anything to do" with it, but his comment there is vague enough to be read either way I suppose.