Indeed, since Lewis had already ordered the overvotes counted, with the totals reported to him, not counting them would have amounted to Lewis saying, "I know you have found these perfectly valid uncounted ballots, but I'm not going to let them count." It wouldn't have been easy to defend that position on the inevitable appeal.
(Keep in mind that Lewis was one of the few straight-shooters in the whole Florida saga. He gave Gore a big victory one day, and then gave Bush a big victory a few days later when he upheld Secretary of State Katherine Harris' decision to ignore some manual recounts. It's hard to dismiss him as a partisan hack.)
Had there in fact been a statewide re-examination of the overvotes, Gore would have won—according to the media recount (which was, admittedly, not precise)—by a margin ranging from 42 to 171 votes.
It's now clearer than ever that, when Ford Fessenden and John Broder wrote confidently that "George W. Bush would have won even if the United States Supreme Court had allowed the statewide manual recount … to go forward," the two Times reporters didn't know what they were talking about.
P.S.: Isikoff's evidence is embarrassing not only to the Times and to Bush (who we now know needed the U.S. Supreme Court) and to Gore (who foolishly didn't ask for the crucial overvotes to be counted). It's also embarrassing to ... Jeffrey Toobin! Toobin wrote an entire, 280-page pro-Gore book about the Florida recount and somehow didn't come up with the crucial evidence that would have made his case. (Why do I have it in for Toobin? Click here, here, and here.)