Since they've always been his kids in both regions until the modern era, I'm going to go ahead and pretend this is evidence for my Yoshi's Island DS split-timeline theory. In the branch created by Bowser travelling back in time to kidnap babies, Mario and Luigi get sent to Brooklyn, and Bowser, traumatized by being kidnapped by an older version of himself, sleeps around a bunch and has a bunch of kids (who just happen to look like (nephews/business associates/whatever) from the non-Brooklynized timeline).
This might mean that the Super Mario Bros. games (at least 3 and World) only happened in the Brooklyn timeline, and the modern-era timeline only includes the New Super Mario Bros.es. This is gonna be fun.