I believe the difference is that in baseball, batter outcome as it relates to change in base-out state is germane to the disposition of the game in a way individual pitches are not. If a pitcher throws a ball outside the zone, that does not change the win probability of the game in any way. Win probability changes only when base-out state changes. In football, throwing an incomplete pass does negatively change win probability.
IOW, in a baseball perfect game, every batter disposed of raises the win probability for the pitcher's team, because it never goes down. But even in a quarterback's "perfect game", when he throws an incomplete game, win probability drops. That is, practically by definition, imperfect.