Puzzles With no Visible Effect

These puzzles do not seem to do anything, nor to teach anything:
 * The two puzzles in the orange container in town, that require to change the color of the lighting to be solved.
 * The puzzle in an underground room of the Marsh (magenta exit of the rotary platform).
 * The puzzle floating on the surface of water in the third underground of the Desert Ruin.
 * Most of the puzzles in the Caves.

This puzzle does not seem to do anything anymore nor to teach anything, but may actually have had an effect in earlier versions of the game: This set of puzzles do not seem to do anything but teaches you a puzzle mechanic: This set of puzzles do something but this seem does not seem to be useful in the game:
 * The puzzle in the Concrete Factory's control room that has a similar layout as the one on the vault door in the Start Area and the one that opens the shortcut door to the caves in the Mine Building in Town. It used to also open the vault's door but this bug has been fixed in a PC update. Solving this puzzle may also have been required to activate the Quarry Elevator in early released versions of the game, even if no wire gets out of it and the cable wired to the elevator is connected to the puzzle that opens one lock of the laser's puzzle (which is also required to activate the elevator).
 * The optional puzzles in the Symmetry Area, where you have to trace lines around rocks and palm trees through the puzzle.
 * The puzzles in the Orchard, that open the door to the bonsai worskhop attending the Windmill.