However the differences are often overstated, and with regards to Japanese culture some people seem to harbor strange preconceptions that make them blind to rather obvious falsehoods, leading to debacles like the New Yorker article described in OP. It goes both ways of course; a lot of Japanese people seem to have bizarre ideas about the US for example, perhaps I would too if I hadn’t lived there for a decade. It’s easy to form a skewed image of Americans if your knowledge only came from Hollywood films.
I’d say that in general, the more years you spend immersed in cultures outside of your own, the more you’ll be able to see beneath the surface and appreciate how similar we all are — for better or worse. Just look at the number of comments in this thread from (presumably) Western expats pointing out how "ordinary" Japan is in reality. That realization comes from actually living here and being directly exposed to the culture. Not from watching anime.