Anyway, I disagree with you: Japan is still a miracle in terms of the quality and service you get for the money. I saw this many times over.
Perhaps not in Kyoto, or in the most touristed areas of Tokyo. Or in whatever random place got featured in some anime, or whatnot.
The article mentions Yamaguchi, Toyama, Morioka, etc., and I definitely agree -- there are tons of places off the tourist beaten-track, and any of them is worth a visit.
On my recent trip I was in Kobe, which unlike Yamaguchi etc. I expect the average HN reader has heard of. But even there, there was little trace of overtourism.
Alex Kerr lamented all the way back in 1993 (in his book Lost Japan) that Kyoto had essentially lost its soul. And if you go to the areas most commonly seen on Instagram and TikTok, that's probably partially true. But even in Kyoto, go off the beaten path a little, and you will find much to delight you!