The article doesn't mention the common Japanese practice where employers pay the cost of their employee's rail passes. This subsidizes expensive, long-distance commutes, and at least some employees would likely choose a cheaper commute if they had to bear the cost directly.

Intercity trains will come with an intercity price tag, which is more than most people are willing to pay for without a subsidy. There's a reason very few people in Europe use ICE trains for their daily commute.