Though I'd suggest that Social Media is causing some very real problems - but I don't see an easy answer that doesn't involve changing the fundamental constructs of social media.
I see different kinds of limitations that are driven by blindly chasing profit, attempting externalize everything that doesn't affect the bottom line, and insistent refusal to accept even partial responsibility for creating tools when said tools are misused until public opinion is overwhelming against them. I don't think that the limitations that I listed are ideological though.
FWIW I do think SF and the peninsula need dense urbanization, but this is due to the geography of the bay and the fact that demand seems to be overwhelmingly outstripping supply, and I'd rather increase density than rip up the green space along the peninsula. I don't think this is necessary for most cities though, or even necessary around San Jose for that matter (since it has less narrow growth constraints due to geography). I get the impression the majority of locals / immigrants in the Bay Area who support denser urbanization have a similar viewpoint, and don't consider it an ideological necessity for the rest of the world.
So the author's point is that the "monoculture of thought" that pervades The Valley (and elsewhere) is in fact a problem, and one that needs to be addressed.
There are different words for the monoculture. Here on HN you might see it referred to as "the hivemind" or "groupthink". Or HN itself might be called an "echo chamber".
I think this is a valid concern, expressed by a voice in the minority, and is worth the time to attend and reflect upon.
To answer your original question, I would say that the harm that Silicon Valley is causing the world is the creation of the hivemind itself. It's not overt; it's insidious.
hack the planet