This "secret ending" https://www.youtube.com/watch?v=-yMw0l26Jvs where he leaves the game and tries to look for the same pattern in the real world but obviously nothing happens. IRL this is like conspiracy theorists who filter all events through their worldview. I remember in college playing so much Katamari Damacy that I couldn't help imagining rolling up cars in the street.
EDIT: Another layer is it's also a game about making games, ways to communicate to the player, and how to make a stripped down interaction scheme rich. I've def found more game developers who like it than non-game developers.
... many of the puzzles have multiple solutions depending on what you want them to activate when you solve them, or on the perspective you have when solving them. I don't think your assessment of the message is very generous.