Fridge Horror: The tragedy that The Samaritan came back to prevent, the one that was the difference between the future being a barren wasteland and a utopia? That tragedy has occurred in our world, meaning we're going down the barren wasteland path...
Except, Kurt's made it quite clear that the future Samaritan came from is just one of a multitude of possible ones. And while he prevented the original Bad Future he came from, some others still exist and can even send people back when the conditions are right. (See the story where Jack-In-The-Box meets his "sons")
Also, the world of Astro City had already been different from ours since at least the 1800s. So they were already on a different path anyway.
Fridge Brilliance: The Samaritan is a Superman expy. In-story, he first appeared in 1986, the year of John Byrne's Superman reboot. Coincidence? I think not.
There are multiples expies for some characters - to represent different, seemingly contradictory interpretations of the character. Leopardman is Silver Age Batman, Confessor is Dark Age urban legend Batman, Black Rapier is Bronze Age Justice League Batman. Supersonic, Atomicus, and Samaritan are a similar set, each giving a different perspective on Superman's history.