The most consequential project in postwar Japanese rail history (not named Shinkansen)
1) This project is not as unique as you might think. I would argue that the RER and Grand Paris Express were/are on a similar scale to what you describe.
2) The premise of what is in this article is widely understood by city planners everywhere, the issue comes with how Tokyo found the space to quadruple railway lines, and how it was able to obtain the loans.
I think this is a fantastic start. However, I think it is remiss in not mentioning Japanese private rail companies and rail integrated development. For example, between Yokohama and Shinagawa, the Keikyu line parallels both the Tokaido line and the Keihin-Tohoku line. However this is fascinating, and a worthy subject of study.
Fascinating story, so well researched & written. Looking forward to Part 2! LBM