If the Auto Import folder is configured to not require entry of any Keyword Values, Keyword Types that are part of a Multi-Instance Keyword Type Group should not be used. Documents can be improperly indexed.
If the Auto Import folder is configured to require entry of any Keyword Values, Keyword Types that are part of a Multi-Instance Keyword Type Group can be used. However, the Multi-Instance Keyword Type Group is not automatically populated. This is a known limitation of the Keywords pane.