It could use maps for Japan and for Tokyo specifically, because the map for Japan is pretty much a unified blob from Tokyo to Hiroshima.

There's an anime called ZatsuTabi, where every episode has the main character go somewhere different, and every place is a real place. It almost feels like cheating.

I would also suggest Syowa Station in antarctica, visited in A Place Further Than the Universe. It's already listed with Singapore, but the station is a real place too.

Edit: Oh! Also, A Salad Bowl of Eccentrics is set in Gifu.

A couple of very random locations otherwise unmarked:

The early episodes of Vinland Saga take place in Iceland, making it, I think, the only anime set there to date. I can't remember whether they ever give a town name or not.

While most of the series takes place in London, England, one of the Moriarty the Patriot OAVs is set in Bath.

What's the anime/manga taking place in Havana?

Edit: Answering my own question after looking at the map (duh): The Millionaire Detective - Balance: Unlimited.

The sheer number of individual anime where the characters have visited (and usually trashed—it was almost a running joke back in the 1990s) the Tokyo Tower boggles the mind, so you should probably mark it with a large star.

solo leveling is in South Korea.

Orb: On the Movements of the Earth takes place in Poland; I don't see it listed. Can't remember if there's a specific city.

Isn't Attack on Titan set on Madagascar?

In Persona 5, at least in the game, there's a short section in Hawaii. Does it also appear in the anime?

A Place Further Than The Universe has some travel in it that you're still missing -- e.g. Fremantle (in Australia), and, of course, Antarctica among other locations.

Do you have Noir which is set in Italy / France?

Surprisingly little anime is set in Siberia.

Cool project!

Utterly unhelpful, but I swear I’ve watched some kind of pirate/nautical themed anime set in the Philippines. I know they mention, and maybe even go to the Philippines in Black Lagoon, but I think it was a different show?

Finally, Turkmenistan being represented in media.