The cost of passenger rail is high in America, because America doesn't build enough rail.
If you try building a single megaproject, nobody knows what they are doing, everything is inefficient, and mistakes will be made. But you learn by doing. If the individual projects are small enough that there are always multiple projects in various stages, you develop and maintain expertise. Then you can build things cost-effectively and finish the projects in time.
> The cost of passenger rail is high in America, because America doesn't build enough rail.
The cost of passenger rail is high in America because America has 11% of the population (read: customer) density of Japan.
(For cities, NYC has 25% lower population density than Tokyo.)