Since the boundaries of nations do change in my science fantasy game wolrd and some regions are disputed territories, I use two, or rather three, hierarchies:
Physical Realm:
- Planets
- Continents
- geographical regions
...
Politcal Realm:
- Large supranational entities (Human dominated UNO vs. alien equivalents)
- nations
- states / subdivisions
- cities
...
Netherworlds / Metaplanes
...
I use relationships quite extensively to show, which region or group belongs to which realm etc.
Only in selecting parent topics for groups I am still somewhat inconsistent, even though I tend to group them under the highest level political realm topic relevant (e.g. political parties and factions, corporations etc. of an empire below that nation, supranational factions and alliances below the corresponding supranational organization).