• Smart people often think social institutions are basically arbitrary and that they can engineer better ways using their mighty brains. Because these institutions aren't actually arbitrary, their tinkering is generally harmful and sometimes causes social dysfunction, suffering, and death on a massive scale. Less Wrong is unusually bad in this regard, and that is a serious indictment of "rationality" as practiced by LessWrongers.
• A case of this especially relevant to Less Wrong is "Evangelical Polyamory".

Agreed except for the part about Less Wrong is unusually bad in this regard. I think it's actually doing better then most gatherings of smart people attempting to reorganize society. Keep in mind lesswrong's equivalent 50 years ago would have been advocating Marxism.

• Atheists assume that self-identified atheists are representative of non-religious people and use flattering data about self-identified atheists to draw (likely) false conclusions about the world being better without religion. The expected value of arguing for atheism is small and quite possibly negative.

Agreed.

• Ceteris paribus dictatorships work better than democracies.

You've never lived under a dictatorship have you? I strongly disagree with the above statement and think it's another good example of your first point.

• Nerd culture is increasingly hyper-permissive and basically juvenile and stultifying. Nerds were better off when they had to struggle to meet society's expectations for normal behavior.

True, however, the previous culture was hyper-conformist, since it was 'designed' to create people intelligent enough to operate machinery but conformist enough to work in an assembly line.