Note that the Times qualified this with: "And there may have been an even more glaring telltale that the F.B.I. did not mention in court filings." (So they were more cautious in that respect than other journalists, unfortunately.) In particular, the government has not acknowledged having used this evidence.
With the serial number of the printer, they can track it through retail channels to the buyer. If someone paid cash, they can review the surveillance footage at the point of sale at the time the sale was made. And when they find you in possession of the printer that emitted the printout, they can conclude you printed whatever it was.
