Tin foil lids are (for manufacturing purposes) 2 dimensional. They can be rolled on as wide or as narrow as needed, and perforated to separate the cups from each other. There is little worry about misalignment or not sealing correctly, as with 'lipped' style lids.
Usually, it's a foil because it's in aluminum. Aluminum is a great oxygen barrier. Oxygen kills the bacteria in yogurt. Some studies pointed out this, so this must be a concern in the food industry. Maybe there are some other reasons, but this is one of those.
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