They're connecting Tokyo and Nihonbashi stations underground which will effective connect 10 stations in total with underground passages so that would be another interesting 3d map

Also, that map seems incomplete by at least a 3rd. The connection between it and Shinjuku-3-chome station is missing (the hallways just arbitrarily stop on that map) and the tunnels from there to the south entrance of Shinjuku station are missing as well as 3 more train platforms. I suppose you could argue that's a different station which is fine, but the fact that tunnels don't end where they appear to on this map is misleading.

Looks like the cutoff is from the source governmental data. It's also missing Tochoumae and Nishishinjuku, even though it has Shinjuku-nishiguchi and Seibu Shinjuku.