Critics of verifiable voting do have a point when they note that the printouts are susceptible to some of the same kinds of tricks once played with paper ballots.
Good article, but he does have to make reference to this point that I've never seen explained anywhere. The point I've always seen made is about the flaws that come up for voter receipts that voters take with them. I don't know of a flaw for the kind of paper trail where the printout is turned in at the ballot station.