Oh, it PROFOUNDLY screws them over, maybe even more than Superman and the JLA themselves. You can at least read a Superman comic and ignore that his place at the foundation of the universe has been kneecapped, but with the JSA that's always going to mean presenting them as the original, primal heroes in a world where they can never, ever actually be the lead (or depending on your feelings on the Titans even secondary) superhero team, or in the case of most of their biggest members the most notable heroes by their own names.