>

There are literal ghost towns in Japan which is the result of younger generations leaving to head to cities for better opportunities.
Pretty sure you'd be able to buy a place in these areas pretty cheap as they'd be crying out for residents again
All the jobs are in Tokyo, so people live in Tokyo or the surrounding prefectures. Now they’re paying people to leave Tokyo and the surrounding prefectures. Where will these people work, then? Japanese companies dislike WFH for, among other reasons, the same archaic reason they all set up shop in Tokyo instead of in other cities: overemphasizing relationships rather than getting the job done.
Try forcing companies out of Tokyo first. Then you might see the population density ease up, up populations of other cities balance out. >

To be fair, there is very decent public transportation in Japan so it wouldn't be terrible. >

It absolutely would.
You can’t just hop on a bullet train and go to work. A ticket costs more than a days wage.
If it’s possible on normal speed trains then it’s probably already inside a massive urban sprawl that doesn’t need population. >

Most rail commuters buy some sort of unlimited pass, prices I've seen for 1-6 month passes come to around 9,000-15,000 yen/month ($68-115)
Which is much cheaper than the 1-time tickets you're referring to. 
For students it's free or at least pretty cheap. >

That's the normal train. Do you want to sit/stand 2 hours to get to work in another city and 2 hours more to go back home, everyday? >

I've personally driven longer commutes (slightly more than 2.5h each way). 
And I didn't get paid for that commute, car, insurance, fuel, maintenance, I had to pay for it all.
And it was a heck of a lot more expensive than ~$100/m
People have different levels of tolerance for inconvenience. >

that mean your works days you had no life at all, why did you have done that to yourself? do you hate yourself or something? >

Being homeless is worse than a long commute. >

1 million yen equals $7,696.65 USD >

Arguably has more buying power compared to US living costs tho >

Idk Japan wasn't quite cheap for me but I'm European. Especially housing (they don't have much space). In Tokyo, you can easily pay $50 a night in a room as big as a coffin >

Though this offer is to leave Tokyo...I wonder if it's cheaper once you leave one if the largest metro areas in the world.