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‘manage_product_terms’ capability is responsible for the product categories. Admin menu window is helpful in such cases.
WordPress does not have a global structure to remember all available meta boxes, as WP does with admin menu. Meta box becomes available when user opens a page for which meta box is created.
Currently URE remembers available meta boxes step by step when you open dashboard or post/page/CPT editor pages. It does not delete unavailable meta boxes automatically. Imagine another situation when you temporarily deactivated some plugin for the debug purpose, but URE deleted all restrictions you made for its meta boxes.
I agree that some cleanup should be possible. What if to add ‘Remove’ link to the right of every meta box in a list?