I'd say there wasn't even a need to bother with timelines until it became untenable to reconcile all of Nasu's works in a shared framework of rules. The core three operated under the same logic of a setting that could accommodate for all their constituent elements; small corrections of that time had to do with potential logical conflicts. When you drop something like Extra on that setting, it doesn't insert neatly into the existing framework; hence, alternate timeline, and a fundamental restructuring of setting.