In both the Flashpoint storyline and Justice League: The Flashpoint Paradox animated adaptation, we find out at the end that the Flashpoint timeline was created by
Barry Allen going back in time to save his mom.
I can maybe understand why this would result in a butterfly effect causing changes to other superheroes on Earth (e.g. perhaps a police officer didn't need to come to the Allen house, so their different patrol route impacted the mugging of the Wayne family).
But I can't understand how this change could possibly impact baby Kal-El's pod landing not in Smallville, Kansas, but in downtown Metropolis. How could this have happened, given that the pod was in outer space when the source of the timeline shift happened?