The article seems to be mostly true in areas with closed communities, like high school, and I'm not sure how much it applies to later social non-success.
Status isn't zero-sum when you can walk away, and while building a network of contacts takes time you would hopefully do so with people you like (who, being nerdy, are more likely to have profitable technical skills).
People ganging up on you because they need something to hold their group together and they know that you don't have many allies is different from people not allying with you because you give off the impression of being someone they don't want to associate with.
Formal schooling creates a hot-house environment for social development: it's artificial and fosters growth of things that wouldn't grow otherwise. The point I want to make with respect to the current discussion is that when nerd types fail to thrive in it in their formative years, it puts them behind in social development, and some have extreme difficulty catching up. Those who never catch up can fail to associate successfully even with other nerd types.
Suppose that you're a bee. Perhaps, even, an extremely rational bee. And yet, as you go through your life, you can't shake the feeling that you're missing something - the other bees live so effortlessly, alighting on flowers bursting with pollen as if by chance. Try as you might, you can't seem to figure out the patterns that they're unconsciously drawn to. Are you overanalyzing? Are you overwhelmed by sensory data? But the others seem to defy thermodynamics in their ability to extract useful information, all the while wasting so much effort on suboptimal patterns of thought.
Perhaps they have access to different data? Perhaps, where you see a uniform field of yellow, they see bullseyes.
Less Wrong seems to have a problem with socializing. Not just an unusual share of the people, but the community's character (as if it were a person). We should suspect ourselves (as a collective) of overlooking the ultraviolet, those facts about the world that are so easily accessed by some others. We should be suspicious of simplistic or monolithic explanations of social reality that don't allow sweeping social success on the same scale as their claims. We should be suspicious of dismissals of social concerns.
Am I off the mark? Am I worried over nothing? Am I overreaching? I am tossing this idea out into the sandstorm of doubt so that it can be worn down and honed to the razor edge at its core, if such a thing exists. I ask you to be my wind and sand.
Disclaimers: I don't intend this as an insult. It's a reminder - as a collective intelligence, we have a blind spot. We shouldn't conclude that there's nothing behind it. I myself am pretty dang "manualistic" (or whatever the other side of neurotypical is called). I am not an apiarist.
Edit: I've removed the focus on Autism. I was wrong, and I apologize. The post may be further edited in the near future.