Of course it really depends on the individual train line and time of day and direction and if it's a holiday etc. If you have enough local experience to know for sure it won't be sold out in advance, then that's great for you, but if you're traveling somewhere new you won't know that.
I'm not talking about commuter rail, which is like what you're describing.
But unless it changed recently, it's not quite like that with the shinkansen in Japan. I would usually buy a ticket in advance for a late time trip around 10pm (with reserved seat), just in case all shinkansen are sold out (never happened, but I'm the anxious kind). On the date of travel when I'm ready to leave I just go to the train station, and ask at the counter to change my ticket for the next shinkansen. It's completely free, including the reserved seat, although maybe that's only for the Nozomi shinkansen? Not sure for Kodama/Hikari. Never had an issue with the next shinkansen being full, but maybe I've just been lucky.
I was mostly traveling between Osaka and Tokyo, where there is one shinkansen every 6 minutes at rush hour, and at worst one every 20 minutes. So in practice the waiting time was practically nil, and I loved the flexibility of being able to decide until the last minute to either dine out in Tokyo with my friends, or simply head back home earlier.
I live in Japan and you absolutely do not need to book trains in advance, ever, for any reason. It's a good idea if you're planning to travel during peak hours on the first and last days of a major holiday period, but there is a free seating area that you can ride. The only downside is that you may need to wait a bit on the platform until you're squeezed onto the shinkansen. You're sacrificing some comfort this way, but it's not a strict need.
But that problem only occurs 3 weeks out of an entire year. Also, the normal free seating tickets don't have a reserved time. They're only limited by day.
And my experiences in Europe are similar. Show up, buy a high speed rail ticket, hop on a train and go to the next city.
I've only ever needed to reserve tickets in two countries: one was dealing with Amtrak in the US, and the other was trying to take a train in China between two cities in the midst of the biggest holiday of the year. Other than that, it's always been a show up, get a ticket, and hop on 5 minutes later sort of deal.
Which is, of course, when you're statistically the most likely to be traveling.
And the fact that a ticket is valid the whole day doesn't help much when your flight is delayed overnight or by a day.
Some people tend to travel precisely when others are not, and might not run into this problem, seems like that might be your case. Other people travel precisely when others are too, and will run into it all the time. As far as China, every hard sleeper I ever took was sold out in advance, zero holidays.
As far as I can tell, you're entirely confirming what I'm saying.
If you book in advance and your plane is delayed by a whole day, your ticket is void. That's it. You're done.
...In which case you can just show up to the station and buy an unreserved ticket and ride, like everybody else and like I mentioned is the better idea.
My point is that reserving in advance has no purpose because of reasons you're giving to somehow justify it. If you don't book in advance, there is zero chance of missing your train due to a delayed flight since you're buying it 5 minutes before riding.
You seem very, very confused.
For a overseas tourist arriving by flight, anyway it's better to avoid the three weeks. I believe it's on May, August, and end of the year, but former two is Japanese local holidays so you can easily avoid. Then you don't always need reservation shinkansen because free sheets are available (but YMMV).
I don't know if you're American, but I think you've just got funny ideas about how trains work. You don't really need an advance booking - you just turn up, buy a ticket, and take the train. It's not a big deal - they go every hour or so between major locations so you don't have to wait long. Trains are more like busses than aeroplanes in most places - Amtrak is an outlier in trying to be like an airline.