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The order of events is always the same. The Zinnia thing was just Gamefreak's way of saying "yeah all version are canon in some universe" so they didn't have to care about continuity any more. FRLG and HGSS didn't change much from their originals, but ORAS with the fairy type shat on some lore (like Whitney's gym) so this is their way to fix things.
That way each person makes a timeline with the version they played and they don't have to declare anything canon because they're lazy. Red only got lucky because when Kanto came out he was the only protag.
