Alternative hypothesis 2
(At this point I should point out that I like your hypothesis, I just think it is not necessarily single-cause)
Satoshi Kanazawa's charmingly simple theory that general intelligence tends to suppress and displace most of your instincts. This means being smart pretty much automatically means being bad at a lot of things. The way I interpret it is that attention is a finite resource and you either pay attention to your analytical engine or your instincts or share it, but you cannot give full 100% attention to both. So if the analytical engine demands your attention the insticts shut up/down.
I have observed intelligent people being bad at the following instinctive things (not all of them, not in all of these):
This may be a case of ignoring people who are bad in both intellectual and physical things. Those people are just not salient, the same way as people think smart people are ugly and beautiful people are dumb. It may simply be that the ugly and dumb people go unnoticed. This is Berkson's paradox: Even if A and B are independent, they are dependent conditioned on (A or B).
I've often heard LWers describe themselves as having autism, or Asperger's Syndrome (which is no longer considered a valid construct, and was removed from the Diagnostic and Statistical Manual of Mental Disorders two years ago.) This is given as an explanation for various forms of social dysfunction. The suggestion is that such people have a genetic disorder.
I've come to think that the issues are seldom genetic in origin. There's a simpler explanation. LWers are often intellectually gifted. This is conducive to early isolation. In The Outsiders Grady Towers writes:
Most people pick up a huge amount of tacit social knowledge as children and adolescents, through very frequent interaction with many peers. This is often not true of intellectually gifted people, who usually grew up in relative isolation on account of lack of peers who shared their interests.
They often have the chance to meet others similar to themselves later on in life. One might think that this would resolve the issue. But in many cases intellectually gifted people simply never learn how beneficial it can be to interact with others. For example, the great mathematician Robert Langlands wrote:
At first blush, this seems very strange: much of Langlands' work involves generalizations of Selberg's trace formula. It seems obvious that it would be fruitful for Langlands to have spoken with Selberg about math more than once, especially given that the one conversation that he had was very fruitful! But if one thinks about what their early life experiences must have been like, as a couple of the most brilliant people in the world, it sort of makes sense: they plausibly had essentially nobody to talk to about their interests for many years, and if you go for many years without having substantive conversations with people, you might never get into the habit.
When intellectually gifted people do interact, one often sees cultural clashes, because such people created their own cultures as a substitute for usual cultural acclimation, and share no common background culture. From the inside, one sees other intellectually gifted people, recognizes that they're very odd by mainstream standards, and thinks "these people are freaks!" But at the same time, the people who one sees as freaks see one in the same light, and one is often blind to how unusual one's own behavior is, only in different ways. Thus, one gets trainwreck scenarios, as when I inadvertently offended dozens of people when I made strong criticisms of MIRI and Eliezer back in 2010, just after I joined the LW community.
Grady Towers concludes the essay by writing: