People are still arguing over whether the Lost castaways were “in purgatory the whole time?” The finale was very clear on that: everything on the island happened. The afterlife didn’t come into play until the final season.
That last season featured glimpses of what looked at first like an alternate timeline in which the plane didn’t crash. It turned out to be a shared afterlife experienced by everyone who had ever been to the island, once they had all died –- some of them during the show, some years later, as Ben and Hurley acknowledged when they regained their memories. And that wasn’t a state of purification so much as a gathering point, so they could all meet again before moving on, because what they’d done and experienced on the island had been so important.
Everything on the island, before the island, and after the island, for all six years of the show, was in the “real” timeline.
The finale may not have answered every question, but it spelled that one out pretty clearly.