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.

I think you're misinterpreting him. All he's saying is that its ridiculous that he simply crosses something off on a calendar and people are acting like he created a brilliant productivity system.

He finds it hilarious presumably because people have been crossing things off on calendars probably since calendars and writing implements both existed at the same time.