it's an amusing premise, but fundamentally flawed in many ways.
there is only one manhattan in north america, and only one new york city... but downtown san francisco comes closer than most other cities and certainly any west of the mississippi.
in this image there are more than 150 towers with perhaps another 20 to come in the next 5 years, including several of more than 50 stories. there is heavy rail transit, grade separated light rail, some of the world's busiest bus lines, millions of square feet of retail, tens of thousands of hotel rooms, etc etc.
to compare this to brooklyn is somewhat ridiculous. very few cities approach this level of density of jobs, housing, and amenities. brooklyn is amazing but it's not really a complete city - it's a part of new york city, integrally connected and mutually reliant on manhattan and to a lesser degree the other boroughs.
like new york city as a whole - but much smaller - san francisco is a complete city, with relatively high density throughout but discrete neighborhoods and districts. it's not a bedroom community no matter how many tens of thousands of people commute out of the city any more than new york city is just because some people work in jersey or connecticut.
where the article has some merit is that silicon valley itself is an uninspiring physical environment. but to compare it uniformly to newer sun belt suburbs is also unfair. within the greater bay area there are older and newer neighborhoods, most of which are relatively dense by sun belt tract standards, and the sheer amount of office space (hundreds of millions of square feet) in the greater bay area is more than anything outside the country's very largest metros.