Suggest an alternative solution to Regions

I have largely completely the structure of our guide to Japan. (https://www.gojapango.com/geodirectory/)

This guide uses the following structure
Regions – Prefectures (similar to States)
Cities – Largely works, but some problems with Tokyo as it has spread out of its Prefecture.
Neighborhoods – Wards or Cities within large urban areas of mega cities.

I am having troubles finding a solution to a few locations/attractions.
Example: Mt Fuji
If anything it is a bit like a region, but formally it actually covers two prefectures. If I made Mt Fuji a region then I spoil the formal structure, but it would allow me to include the surrounding cities, towns and attractions that are focused around Mt Fuji.

I am not sure if tags could be used, but I can’t see how as the widgets for all the other cities are not set up using tags.

Suggestions?