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Version 1.84 - Unity 6.1 - Interface (Menu, inventory) and cursor not Working
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Keeping things in the same scene will make it easier to register the effect of completing the puzzle, i.e. unlocking a door. Other than that, though, it's more a case of personal preference.
When creating a new scene, you have the option of overriding its camera perspective - so if you needed a puzzle to be 2D, with 2D colliders, you could have a 2D-only scene just for that puzzle.