The ZYX Term Meta allows any term of any taxonomy to have any number of parent terms (even if the terms belong to a taxonomy that is not hierarchical) with term metadata.
The widgets included in the plugin already can display and use this alternative hierarchy (or disable it, if you want), but most themes will need a bit of code in its templates to display posts with the multiple parentage enabled. The Proteus theme, included with the plugin, already has full support for multiple parentage.
The exact bit of code that you need to add to your category/tag/taxonomy template is different, but not hard nor long (most times, just a line or two): the API does all the hard work. The exception is the taxonomy template cases, due to the extremely poor support that is offered in WP_Query class to custom taxonomies, compared to the terms of regular category or post tag taxonomies.