This is an excellent visualization! I would love to see someone adapt this data into a first-person navigation game. The game should put you at some location in the station complex and ask you to navigate to some location. This would be excellent training for people visiting the real-life Shinjuku station for the first time.
I thought the horror game "Exit 8" was going to be like that when I bought it: having to navigate through a labyrinthine nightmare version of Shinjuku or Shibuya station, trying to remember the passageways and —hey wait... was that escalator there before?
Turns out is was the opposite since the whole game takes place in a single hallway. It was still a lot of fun though!
https://en.wikipedia.org/wiki/The_Exit_8