You score a TD with 31 seconds to go, as Estime did. You kick the extra point or fail to get the 2-point conversion. The other team has, say, a 6% chance to score a TD and win the game, so your chances of winning are now 94%. If you go for 2 and get it, other team may now have a 4% chance of winning, and yours are now 96%. Combined we're looking at about a 95% chance of winning if Estime scores a TD.
You fall down at the 1. Duke has 3 timeouts left and has to burn one. You run 3 more plays, and let the clock run down to maybe 3 seconds left, Duke has no timeouts left. Your kicker kicks what basically is an extra point and he makes these 97% of the time, so you have a 97% chance of winning doing it this way. And 97% > 95%.
Maybe Duke's chances of scoring a TD and winning in OT were less than 3%, but that's undoubtedly low. So Freeman is right, the analytics dictated ND would have a better chance of winning had Estime fallen down at the 1.
This is not hard to understand. But as I said, analytics doesn't take into account game flow. Maybe Shrader in this tense situation is only 85-90%, who knows? Either way, ND had a great chance to win at this point.