I’m answering your original question here as I had to solve the exact same issue. “How can I map the same entity to different slot”.
You can solve this with new FormAction with slot_mapping.
In NLU, you can just train “country” entity only.
Then, in FormAction, you define both as required_slots like this return ["origin", "destination"].  then in slot_mappings, you define like this
return dict(
            origin=self.from_entity(entity='country'),
            destination=self.from_entity(entity='country')
        )