Fridge Brilliance: The Turtle and the Pebble joke the townsfolk start talking about towards the end of the game. Sure, at first it just seems like something fun the developers added to make you talk to the townies, in hopes of figuring out what the punchline is. Then once you make the Sword of Gear the Gearman reveals that the punchline was 'removed' from the world because the person it was supposedly about wasn't happy about being made fun of. You laugh, feeling a little disappointed, but then you realize just who would have that ability, and this comes the Fridge Brilliance: Beiloune is the Turtle, Princess Marlene is the pebble, and the true Marlene is the baby turtle.
To build on that, when you hear the rest of the story,or at least what didn't get erased, from the the villagers you'll hear that a red turtle enters the story and directly challenged the mother turtle about the pebble she's claiming to be her child. Note that the red turtle is the only animal with the guts to actually do this in the story and compare him with who in the game was most resistant of the classification system and the red turtle is Ari.
Fridge Horror: The "god" of this world created categories (read "castes") for people to live in for their entire lives. Beiloune's motivations read eerily similar to the type of "logic" the [whatever]-ist type of people tend to make: "Everything in the world would work just fine if everyone stayed in their place!"