The field notes that unlock after Zadnor suggest that the story is done and dusted as it explains that virtually all of the loose threads end up getting resolved some months after the events of Zadnor...which likely also puts them well after any of the future MSQ bits so it seems unlikely we'll actually have any hand in the future of Bozja and Dalmasca from this point forward unless there's a timeskip after 6.0 or something.