Playing Japanese video games in my youth also introduced a strange sensation whenever urban settings were involved. It always felt like the Japanese intrinsically did not get how cities worked. They were spotless, cleansed of dirt, strange toy sets based on an idealised view of what a new city out of the box should look like.
Especially in horror games or games involving darker settings, this was just plain bizarre. If you've played the Earth Defense Force games, you might have encountered this strange feeling: the city as it starts feels eerily trapped in uncanny valley and only when everything is reduced to rubble is there a semblance of a lived-in quality shining through.
Then I actually visited Japan.
Osaka is often described as being one of the most polluted cities in Japan, but blimey... it was clean. Streets, alleys, side walks, it didn't really matter what I looked at, everything was clean. The notion of trash is almost an alien concept. Apart from collection zones for trash bags, finding an actual trash can was nigh impossible. The ones you generally do find are companions to vending machines, awaiting emptied cans or the sort, but other trash... well, good luck in binning it somewhere outside of your home.
The thing is, you kind of get used to it real quick. Returning to Schiphol Airport in the Netherlands and taking the last available train back to my home town, I was appalled at how dirty the train car was. The contrast was just immense and a sort of reverse culture-shock set in.
According to this BBC article, it seems this sense of cleanliness is baked into the Japanese mindset at a practical and mindful manner. It also explains the strange condition called Paris syndrome. Japanese tourists can have a highly idealised view of the City of Love and once they actually visit Paris it turns out the inhabitants are rude and the city itself is a smelly trash heap which happens to have all these classical artefacts strewn about. It's heartbreaking to them to visit the perfect city and find it to be its polar opposite. (I mean, even to my trashy senses, Paris is one of the grimiest places I've ever visited.)
These days I tend to look at clean video game cities in a different light. They now not only signify a clean place, they also subtly indicate that whatever this city is supposed to be, its a Japanese place at heart. Likewise, I now often wonder if the Netherlands could be just as clean if we really wanted to.