What about games like Mario Golf / Tennis or Pokemon TCG, where you don't really have "towns", just one or two large areas where you can interact with NPCs? Or even Zelda, where there are various areas outside of towns that still have people in them?
For both of those cases I would say no, it should be an actual town.
For Deus Ex type stuff, it should basically be where the towns are "separate", don't you think?
What about "town-like" stages on side-scrolling games, for instance ?
Megaman X opening stage is a city. The rest of the game isn't. Revenge of Shinobi has two clearly city stages, Chinatown and the street. Does that count ?
MMX opening stage is all combat, no peaceful NPCs. I don't know about Revenge of Shinobi but I get the feeling it's the same.
So, no. Unless the stage is a break from the combat and you're talking to NPCs there (I think Mega Man ZX games have done this?), it's not a "town."