As I understood, lots of Japan is rural, and travel between places outside of the main cities and tourist spots is limited. It'd be like saying the US has good public transport because of the NY subway...
I got out to the middle of fucking nowhere on a mountain by taking the Shinkansen, then a local small train, then a bus, and finally a taxi because I didn't want to wait 20m for a shuttle bus
Compared to California (home, comparable size and layout tbh) it's way easier to get to remote places period thanks to the public transit system
Quite literally to do the same trip I did in Japan in CA I'd have Maybe a slow ass Amtrak line to get me close-ish in twice the time of the Shinkansen and still have an hours drive of my own rented car to get there
I’ve traveled from tiny towns in northern Japan to major cities like Tokyo. All on public transportation. Bullet trains, local trains, they’re very well connected to each other.