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You can use whatever you like for the preferences. Prefs are just a dictionary serialized to a json file. You can create your preferences as a dictionary of dictionaries, or as a dictionary of lists, or as a dictionary of lists of tuples if you like. It's just up to you to make sure the structure is properly populated before you save the preferences. Just like it's up to you parse the structure after retrieving the stored preferences.
I tend to use a dictionary of simple dictionaries, myself. Mostly for common grouping purposes. I've not really encountered a situation where complicating it much further than that would be an advantage. Your mileage may vary, though.
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