The scenarios you listed are explaining how to handle any payments made with form 4868 once you actually file your tax returns.
Scenario 1: If you filed separate forms 4868 and made payments and then decided to file a joint return, you would include on your joint tax return both (any) payments made with the separate forms 4868.
Scenario 2: If you filed a joint 4868 and made a payment and then decided to file separate returns, you could split the joint payment amount however you agree or one of you could include the entire payment on your separate tax returns.
Scenario 3 (Not listed): If you file a separate form 4868 and file a separate tax return, you would include only your separate payment on your separate tax return.
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