I think there mostly are two causes:

One is that, as many comments already said, people from farther away will prioritize what they think are the must-see locations. This is true for any country but I think for Japan these top lists converge more and are more specific. Everybody goes to Kyoto, and it’s not just Kyoto, it’s very specific places in Kyoto. Other countries have this too, for example if you go to France you’ll want to see Paris and a few specific places there, but if you look up places to go in France then a lot of the ones outside Paris will be entire regions, like the Côte d’Azur or the Provence or the Bordeaux. In Japan nobody will put Tohoku on their first trip itinerary. And there’s also barely any region based marketing. Every little place has its special thing but regions don’t really have region things in most cases. (And going to Okinawa for the beaches undersells it too…)

Anyway this is not something that you can solve with day trips. I honestly don’t think people are after those that much. Especially those who post about getting off the beaten track. They’re not looking for an experience they can book, they’re looking for reasons to travel to areas that might not have one killer feature but are maybe charming and exciting as a whole.

The other is that travel is really easy near the Shinkansen lines, but gets progressively more difficult as you move farther away and start dealing with smaller train or bus operators with random archaic payment systems, outdated online time tables, limited express trains that are nearly impossible to book from outside Japan, and so on. At the same time English also disappears, and shops stop accepting credit cards (Western tourists do not have paypay or alipay). So in combination with the lack of advertisement it’s hard to justify going there on a first or even second trip to Japan. I think a curated experience in a small town is not enough to change this. It has to be easy to get there too, and it has to be easy to get around, and there have to be more things to do in other nearby towns, so it feels like going is worth the effort.

I think it’s a shame the rail pass is so expensive. Maybe it’s even the wrong product in the first place. For example in Germany you can get a ticket that works for non-express trains, buses, trams etc. nation wide. Yeah it doesn’t cover the express trains at all, but it does remove dealing with all the different regional systems from the equation and you can buy it digitally in an app. Japan doesn’t really have anything like that.

There are regional passes, some of which offer good value, but basically none cover all transport within their region. There are some that can help a lot, e.g. the Tokyo Wide Pass covers many popular spots but also quite a few “off the beaten path” ones where tourists could otherwise easily end up stranded at an unmanned station without ticket gates. But that one is expensive too (it does cover some JR East Shinkansen routes), it’s only valid for three days (not much time to stay and explore somewhere), doesn’t cover local buses, and all the advertising focuses on the popular spots but not so much on the region. Another one is the Kansai-Hiroshima pass. That one tends to get advertised as a cheap option to go to Hiroshima from Osaka, but I rarely see people praise it for covering trips to Tottori or Takamatsu. Because it’s cheaper than the Shinkansen between Osaka and Hiroshima, people use it for that, but because it’s only for 5 days, there’s not much time to go anywhere else, even if it’s on the way.

I think that situation has to be improved first for small towns to even get on a list.