I am NOT disagreeing with anything above, but I want to add another perspective.
Maybe Atlanta was smarting from their quick knockout the year before? Perhaps they saw that winning the SS would make them face either their nemesis and late charging Crew or the revitalized DCU, in their first round. While not winning the SS would make them face either NYCFC or PU. Any reasonable MLS fan would realize that both NYCFC and PU are better matchups than either the Crew or DCU.
And they needed a well rested Almiron. So Almiron gets a big rest before the playoffs. Maybe he was injured, maybe not. In any event he did not play against Toronto FC in their last regular season game. Nagbe is no Almiron and they lose to Toronto.
So maybe they took their foot off the gas, let NYRB win the SS, and then went full throttle in the playoffs.