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This is confusing: http://cld.wthms.co/134fk/4ViqL7Ni
Using this filter: https://github.com/WordPress/WordPress/blob/5025f72fd32addc4f5a4b7cdf899899ea0734573/wp-admin/includes/nav-menu.php#L227, we can rename the taxonomies in the screen options and meta boxes: http://cld.wthms.co/1jI6V/LX5JITn4.
This comes up a bit in the forums, so I'm thinking this could help lower the support need. Screen options is still widely under-used, so maybe it'd be worth adding some type of link here that will trigger the screen options to open? http://cld.wthms.co/11LR0/47ktudnG
Like "Looking for WooCommerce Categories or Tags? Click here."