For the Battle Maison and Battle Factory, GameFreak simply copied the data over from ORAS / HGSS respectively simply because it would be less work for them. These places have no significance to the in game storyline, so the trainer names and such are not important. So I guess, in your terminology, they are "cloned."
As for reoccuring characters in games such as Cynthia, Professor Oak, and Caitlin, they are meant to represent the same person, or as you call it, "shipped."