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First of all, there is no such thing as "commuter rail", because commuting is a user pattern, not a train service.
Shinkansen lines are used to commute. Same for ICE trains, between specific stations.
The reason why Japan had this specific subway design is due to consideration of the local characteristics:
>Max speed of 130 km/h in all lines due to narrow gauge and mountains
>Historic prohibition of railway lines inside the perimeter of the Yamanote Line
>No such exception for "underground lines" like happened in London, which had the same prohibition.
This led to a large extent of lines going toward the city with little distribution (the same as in London, except without the tube), and they did exactly what London did to expand the tube after the war, built alongside the long distance lines.
All over ground sections of the London Underground ("subway") were created to use pre-existing "railway" ROW, the only difference is that such railways had already gone bankrupt, so you couldn't get the "Joban line experience" of seeing a subway alongside a long distance train because the long distance train wasn't running there anymore.
Note the grey line alongside the Central line (red), and the one connecting the Northern Line at Highgate to Finsbury Park. The "commuter rail" company gone bankrupt and sold the ROW to LU.
