The linked article focuses on the physical features of Tokyo. For me, even more attractive is the economic dynamism that they enable.
I moved to Tokyo in 1983 and have lived there and in nearby Yokohama ever since. Until 2005, I worked as a freelancer—mostly translation, but also advertising copywriting and other related occupations. I did my work at home, but I was often out and about in Tokyo to visit clients, attend narration recording sessions, visit libraries and bookstores, buy computer supplies in Akihabara, etc. Over the years, I interacted with hundreds of other people working freelance in the city: graphic designers, fashion designers, recording engineers, narrators, musicians, editors, photographers, videographers, other translators and writers, and various kinds of agents who made their living bringing together other freelancers to work on large projects. Our meetings would be held in coffeeshops, in taxis, on benches in train stations and parks, and in offices on upper floors of the zakkyo buildings mentioned in the article.
In those days, before the Internet changed everything, that kind of freelance work and lifestyle seemed to be possible only in a city like Tokyo. I don’t think any other city in Japan, except maybe Osaka, had a large and diverse enough population to create a similarly productive dynamism. I, at least, was certain that I would not have been able to get as much high-paying, interesting work if I had not lived within commuting distance of central Tokyo.
Since 2005, while still employed in Tokyo, I have been working in academia and have lost touch with that freelance economy. The Internet has probably made it even more dynamic in some ways, but I suspect that it depends much less on the physical urban landscape.