This is interesting, but not great Japan advice. I just went and had a blast and did the opposite of his advice. I think people are different and want different things and don't feel bad if you just want to see the standard Japan checklist. His talk of everyone being surly..you know what, be respectful, everyone in Japan is so polite and nice that you will be happy with the level of service everywhere.
I've been many times and there is a time to venture out and there is a time to enjoy what everyone enjoys and both are fine.
Yeah, I have spent a year in Japan and visited most prefectures and disagree with the article. Of course you should get off the beaten path, but if you avoid it like the article recommends, you will have a much worse time.
Additionally, the advice to visit Gifu is terrible. I spent a week in and around Gifu-shi per Patrick's advice years ago and, while the area is charming as the article states, it is not somewhere you should visit before seeing a dozen other places.
Gifu is charming, but I don’t get this either. I had a friend there, so my experience is different, a good place to eat, hang out, not really a tourist place even with the castle (and you could see a better one in Osaka).
It reminded me of Milan: a lovely place to live, but a pointless place to visit as a tourist. And I'm at least a CEFR B1 in the language - it would be an atrocious place to visit if you have no Japanese. No clue why the article recommends it (except maybe as an attempt to establish credibility).
I've been many times and there is a time to venture out and there is a time to enjoy what everyone enjoys and both are fine.