I've traveled all 47 prefectures of Japan, and done all sorts of "edgy" stuff that AtlasObscura has yet to cover, such as trails where only several dozen people have crossed that season. I've also revisited tourist hotspots like Kiyomizu-dera in Kyoto several dozen times.

I'd recommend people follow the beaten path. Is the most touristy spots in Japan and Kyoto "overrated" (given how popular it is)? Yes. But if you take out the crowds, is it grander and more significant than obscure site seeing spots off the beaten path? Yes. Efficient Market Theory applies to site-seeing places, especially with the internet.

There is a tendency in SV and on HN to be contrarian, but there's a good reason touristy places are popular. You get the most value for your time, especially if traveling is an expensive luxury for you and you don't want to take the risk. The best travel experiences I had in Japan were in obscure places, but the reason I've been lucky is that I went to hundreds of obscure places, most of which were duds.
Popular places have also been vetted by other foreigners plus the feedback loop of the business ecosystem being ready to handle a wide range of tourists.

Take restaurants for instance. The Japanese taste palette is rather muted/bland compared to what Americans are used, and even most other Asian countries. Consider how Japan only has two Hai Di Lao restaurants, a relatively pricy restaurant for most of the population, while a much lower income country like Vietnam has at least 10. Sure, there are some things that are "objectively" universally loved, let's say sushi, but the random Japanese hole in the wall with a line of locals waiting might be interesting, but not necessarily delicious, to a foreigner. If you read the Google Maps review for restaurants, you'll find two separate ratings distributions between English-writing reviews and Japanese reviewers. There's also a matter of price sensitivity. When you've already spent the fixed cost on flights, accommodations, you might as well make the most of your trip and try the best of the city has to offer. It's kind of outside the sunk cost fallacy. If you're living there, it's not financially sustainable to eat a Michelin star restaurant everyday. You'll evaluate restaurants based on relative value, wherein you have the option and leisure to go to tens of thousands of other restaurants, whereas a traveler only gets a few shots. At any rate, if you follow the beaten path for restaurants recommended by foreigners, you'll likely like it. If you pursue restaurants that Japanese people like, sure, you'll get some arguably authentic Japanese food for the experience but doesn't necessarily mean you'll enjoy it day in day out.

Personally, I would never go to the Ninja restaurant OP mentioned, as my taste palette has been calibrated to the Japanese. It's just screaming tourist trap. There is nothing wrong with that since the "tourist traps" in Japan are still pretty good. I just know it'll be over-priced. If I wanted Ninjas, I'll just go Mie prefecture where they incubated. But if you're visiting Tokyo, power to you for checking out the Ninja restaurant. If you're visiting Kyoto, I recommend "Menbaka Fire Ramen". The Japanese locals I know in Kyoto would not spent that kind of money ($15?) on ramen, especially one they think is way too salty, but I just took a guest who was visiting and it's been their favorite ramen shop in Japan.