If the final game of the season (or two or three or even more depending on the standings), they're meaningless. Why in the world would you waste your best pitching on a meaningless game if the playoffs start either the next day or day after that?
Of course the Padres and Mets pulled back in those games. They'd have been extremely stupid not to. But what in the world would your "solution" do? Why would that change a thing in strategy? The Mets would need their best pitching even more if they started down a game, and the Padres certainly wouldn't want to waste pitching just for fun.