The definition of the extents of a city is completely arbitrary. For example Manhattan is only part of a city, yet the authors don't even blink at treating it alongside cities that are located all around a hilly harbor with extensive sprawl (Sydney) or that constitute an entire country (Singapore).
This paper is more than anything a showcase for the method they created. I think the point of their visualisations is to make them as appealing as possible, and people want to see how Manhattan looks, but they might now want to see how a certain neighbourhood in Singapore looks. And that choice definitely did help create virality for their research a few years back.
The extent is also culturally specific. In America, Sydney could be regarded as multiple cities. Likewise in Australia, Dallas-Fort Worth would be regarded as a single city.
