> I’m still at a loss as to what caused this dynamic. My best guess is that the city developed alongside a mature, well-supported rail system that could whisk people from one part of the city to another, so the advantage of being in the middle of it all was lower. Manhattan’s subway system could be described in much the same way though, so this answer is not satisfying.

I think the author is correct in saying that it's due to the rail system. The difference between Tokyo and New York is that the Yamanote line runs in a circle, whereas Manhattan's subway lines don't.

The Yamanote line not only connects most of Tokyo's major districts (Shinjuku, Shibuya, Ginza, Ikebukuro, etc.), but it's also the line that connects other train lines together. It's kind of like the beltway/orbital/ring road of a typical American city, just that it's a railway not a freeway. My understanding is that after WW2 when the city was being rebuilt, it was a conscious decision not to define a central neighborhood, and instead have all the lines connect to any station on the Yamanote line instead.

Note that this is not a Japanese thing - Osaka's tall buildings are clustered around Umeda, and Nagoya's are in the area around Shin-Nagoya station. Those cities also don't have a central circle line like the one Tokyo has.