Hmmm...when you can first save the game, huh...That guy in the Mayor of Truce's manor tells you that save points are places where the planet's memory gathers or something, doesn't he? I wonder if maybe the Arena could be connected to Chronopolis...it seems like they might have had access and...did they populate El Nido with the monsters there, maybe?
I wonder if the Lost Sanctum could be their way of saying that Crono & Co. were actually responsible for the Reptite dimension continuing to exist...