1. Bond posits Yudkowski thinks that racism is mostly due to genetic difference, and not about the deliberate, mostly political disenfranchisement of minorities.
You say this is a wrong because his appraisal of the situation as being caused by genetic disparities is benevolent, and that he wants to work to "fix" it.
These aren't in contradiction- to say that it's unfortunate that society is racialized, but that it's due to traits rather than politics, is better than being wantonly racist, but still a well-known form of fallacious racism. Some would say this latter one is actually worse in terms of perpetuating the situation.
2. Of course it's "controversial from the get go". He looks at the disproportionate representation of certain people in ie: tech, and concludes that it's because they're "more competent". Nothing here seems to be a counter, you're just basically saying "it's politically incorrect so it's probably right".
3. Clearly it's just a story. This point eludes exactly nobody. The whole point is that these kind of people find these questions ("is rape really bad?") really intriguing rather than obvious. It makes you wonder about the power of Bayesian reasoning- the exact point of the essay.
I think you're too uncharitable to critical writers like Bond (it took me a while to acquire a taste for this vicious kind of writing), underestimating their and their audiences' understanding. As a result, you think this context adds way more than it does.