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The problem with taxonomy as opposed to other core fields is that it is basically a reference field; however, most vocabularies treat them as literal properties, not as items.
If we were using the Drupal mental model to expose the data, the mapping would be on the taxonomy term entity configuration form (which I don't think exists anyway). If we use the mental model that microdata vocabs generally use, the mapping would be on the field itself.
I think we should have a specialized mapping form for taxonomy fields. It should give all of the taxonomy term's properties on the field (instead of the entity) and give a checkbox for people to make this an item instead if people want to. This is a special case that doesn't make sense when you actually have a proper conceptual model of how the code works, but should be more intuitive for the end users.