Japan certainly does not have higher car ownership than the US. It depends on the source you use, but the US is somewhere in the 90s and Japan somewhere in the 60s. Plus they just use them a lot less as you mentioned.
The main issue is people want to copy Japan by building high speed rail, but Shinkansen isn’t actually that useful - it doesn’t carry mail/cargo, can’t carry much luggage, and though pleasant to use it’s quite expensive. It’s closer to business class flights than anything else. Economy class flights inside the country are often actually cheaper if you don’t mind going to the airport.
Japan’s strength is that you can take yourself everywhere daily on a train or walking/biking, and there’s density and malls in the train stations.
Shinkansen is comfortable than airline, no annoying inspection, almost no wait, and utilization is high enough. So technically it should be priced higher than airline, but I also feel it's weird that high CO2 emission airline is cheaper than lower emission train.
For whatever reason (probably just inertia), JR has been highly resistant to adopt dynamic pricing, so Shinkansen tickets costs the same regardless of whether you travel at absolute peak or when the trains are rattlingly empty. This is starting to crumble at the edges a little bit, and I expect advance-purchase fares to plunge if they ever do make the leap.
Yes it's one of the reason to choose airplane for individuals. Govt's regulation for train is an another reason why dynamic pricing aren't done well but it's changing. Currently train+hotel Dynamic Package is available as a cheaper option, but it's not for single day use.
Oh, neat, I recall a trial of that but didn't realize it was rolled out permanently. And apparently you can even book tickets online without jumping through insane hoops! Huzzah!
Yes, it’s competitive with airlines but it’s often more expensive. This makes sense as it’s nicer, but I think people looking at the system from overseas don’t realize this. That might also be due to how good the unlimited flat rate tourist passes are.
Besides renting/owning a car, the real cheap option for intercity travel is night buses.
Japan’s strength is that you can take yourself everywhere daily on a train or walking/biking, and there’s density and malls in the train stations.