I think there will be a negotiated settlement between Baseball and Players on reduction of regular season games versus increase in playoff games.
You make a good point about this realignment's effect on playoffs, though. Baseball would prefer both New York teams and Boston (as well as Los Angeles, San Francisco, and the Cubs) to be in the playoffs every season. These are the teams that reliably generate the most national interest, and thus revenue.
Manfred and the owners speak from one position. He works for them, so they work together, and so if Manfred is saying this stuff publicly, that means he and the owners have already agreed on it privately. As a lawyer, he is careful with his proclamations and would never say anything that would catch his constituents unawares. And say what you want about Manfred, but he is nothing if not careful about what he says publicly as it relates to his owners' wishes.