Let's look at some of your references. You say that Scott has endorsed eugenics; let's look up the exact phrasing (emphasis mine):

Even though I like both basic income guarantees and eugenics, I don’t think these are two things that go well together – making the income conditional upon sterilization is a little too close to coercion for my purposes. Still, probably better than what we have right now.

"I don't like this, though it would probably be better than the even worse situation that we have today" isn't exactly a strong endorsement. Note the bit about disliking coercion which should already suggest that Scott doesn't like "eugenics" in the traditional sense of involuntary sterilization, but rather non-coercive eugenics that emphasize genetic engineering and parental choice.

Simply calling this "eugenics" with no caveats is misleading; admittedly Scott himself sometimes forgets to make this clarification, so one would be excused for not knowing what he means... but not when linking to a comment where he explicitly notes that he doesn't want to have coercive forms of eugenics.

Next, you say that he has endorsed "Charles Murray, a prominent proponent of racial IQ differences". Looking up the exact phrasing again, Scott says:

The only public figure I can think of in the southeast quadrant with me is Charles Murray. Neither he nor I would dare reduce all class differences to heredity, and he in particular has some very sophisticated theories about class and culture. But he shares my skepticism that the 55 year old Kentucky trucker can be taught to code, and I don’t think he’s too sanguine about the trucker’s kids either. His solution is a basic income guarantee, and I guess that’s mine too. Not because I have great answers to all of the QZ article’s problems. But just because I don’t have any better ideas1,2.

What is "the southeast quadrant"? Looking at earlier in the post, it reads:

The cooperatives argue that everyone is working together to create a nice economy that enriches everybody who participates in it, but some people haven’t figured out exactly how to plug into the magic wealth-generating machine, and we should give them a helping hand (“here’s government-subsidized tuition to a school where you can learn to code!”) [...] The southeast corner is people who think that we’re all in this together, but that helping the poor is really hard.

So Scott endorses Murray's claims that... cognitive differences may have a hereditary component, that it might be hard to teach the average trucker and his kids to become programmers, and that we should probably implement a basic income so that these people will still have a reasonable income and don't need to starve. Also, the position that he ascribes to both himself and Murray is the attitude that we should do our best to help everyone, and that it's basically good for everyone try to cooperate together. Not exactly ringing endorsements of white supremacy.

Also one of the foonotes to "I don't have any better ideas" is "obviously invent genetic engineering and create a post-scarcity society, but until then we have to deal with this stuff", which again ties to the part where to the extent that Scott endorses eugenics, he endorses liberal eugenics.

Finally, you note that Scott identifies with the "hereditarian left". Let's look at the article that Scott links to when he says that this term "seems like as close to a useful self-identifier as I’m going to get". It contains an explicit discussion of how the possibility of cognitive differences between groups does not in any sense imply that one of the groups would have more value, morally or otherwise, than the other:

I also think it’s important to stress that contemporary behavioral genetic research is — with very, very few exceptions — almost entirely focused on explaining individual differences within ancestrally homogeneous groups. Race has a lot to do with how behavioral genetic research is perceived, but almost nothing to do with what behavioral geneticists are actually studying. There are good methodological reasons for this. Twin studies are, of course, using twins, who almost always self-identify as the same race. And genome-wide association studies (GWASs) typically use a very large group of people who all have the same self-identified race (usually White), and then rigorously control for genetic ancestry differences even within that already homogeneous group. I challenge anyone to read the methods section of a contemporary GWAS and persist in thinking that this line of research is really about race differences.

Despite all this, racists keep looking for “evidence” to support racism. The embrace of genetic research by racists reached its apotheosis, of course, in Nazism and the eugenics movements in the U.S. After all, eugenics means “good genes”– ascribing value and merit to genes themselves. Daniel Kevles’ In the Name of Eugenics: Genetics and the Uses of Human Heredity should be required reading for anyone interested in both the history of genetic science and in how this research has been (mis)used in the United States. This history makes clear that the eugenic idea of conceptualizing heredity in terms of inherent superiority was woven into the fabric of early genetic science (Galton and Pearson were not, by any stretch, egalitarians) and an idea that was deliberately propagated. The idea that genetic influence on intelligence should be interpreted to mean that some people are inherently superior to other people is itself a racist invention.

Fast-forward to 2017, and nearly everyone, even people who think that they are radical egalitarians who reject racism and white supremacy and eugenic ideology in all its forms, has internalized this “genes == inherent superiority” equation so completely that it’s nearly impossible to have any conversation about genetic research that’s not tainted by it. On both the right and the left, people assume that if you say, “Gene sequence differences between people statistically account for variation in abstract reasoning ability,” what you really mean is “Some people are inherently superior to other people.” Where people disagree, mostly, is in whether they think this conclusion is totally fine or absolutely repugnant. (For the record, and this should go without saying, but unfortunately needs to be said — I fall in the latter camp.) But very few people try to peel apart those ideas. (A recent exception is this series of blog posts by Fredrik deBoer.) The space between, which says, “Gene sequence differences between people statistically account for variation in abstract reasoning ability” but also says “This observation has no bearing on how we evaluate the inherent value or worth of people” is astoundingly small. [...]

But must genetic research necessarily be interpreted in terms of superiority and inferiority? Absolutely not. To get a flavor of other possible interpretations, we can just look at how people describe genetic research on nearly any other human trait.

Take, for example, weight. Here, is a New York Times article that quotes one researcher as saying, “It is more likely that people inherit a collection of genes, each of which predisposes them to a small weight gain in the right environment.” Substitute “slight increase in intelligence” for “small weight gain” in that sentence and – voila! You have the mainstream scientific consensus on genetic influences on IQ. But no one is writing furious think pieces in reaction to scientists working to understand genetic differences in obesity. According to the New York Times, the implications of this line of genetic research is … people shouldn’t blame themselves for a lack of self-control if they are heavy, and a “one size fits all” approach to weight loss won’t be effective.

As another example, think about depression. The headline of one New York Times article is “Hunting the Genetic Signs of Postpartum Depression with an iPhone App.” Pause for a moment and consider how differently the article would be received if the headline were “Hunting the Genetic Signs of Intelligence with an iPhone App.” Yet the research they describe – a genome-wide association study – is exactly the same methodology used in recent genetic research on intelligence and educational attainment. The science isn’t any different, but there’s no talk of identifying superior or inferior mothers. Rather, the research is justified as addressing the needs of “mothers and medical providers clamoring for answers about postpartum depression.” [...]

1. The idea that some people are inferior to other people is abhorrent.

2. The mainstream scientific consensus is that genetic differences between people (within ancestrally homogeneous populations) do predict individual differences in traits and outcomes (e.g., abstract reasoning, conscientiousness, academic achievement, job performance) that are highly valued in our post-industrial, capitalist society.

3. Acknowledging the evidence for #2 is perfectly compatible with belief #1.

4. The belief that one can and should assign merit and superiority on the basis of people’s genes grew out of racist and classist ideologies that were already sorting people as inferior and superior.

5. Instead of accepting the eugenic interpretation of what genetic research means, and then pushing back against the research itself, people – especially people with egalitarian and progressive values — should stop implicitly assuming that genes==inherent merit.

So you are arguing that Scott is a white supremacist, and your pieces of evidence include:

• A comment where Scott says that he doesn't want to have coercive eugenics
• An essay where Scott talks about the best ways of helping people who might be cognitively disadvantaged, and suggests that we should give them a basic income guarantee
• A post where Scott links to and endorses an article which focuses on arguing that considering some people as inferior to others is abhorrent, and that we should reject the racist idea of genetics research having any bearing to how inherently valuable people are

I see discussion of the "eugenics" claim. I don't see any discussion of the "openly endorses white supremacy" claim. What's the evidence for that one?

Much of this argument could be short-circuited by pulling apart what Scott means by 'eugenics' - it's clear from the context (missing from the OP's post) that he's referring to liberal eugenics, which argues that parents should have the right to have some sort of genetic choice over their offspring (and has almost nothing in common with the coercive "eugenics" to which the OP refers).

Liberal eugenics is already widespread, in a sense. Take embryo selection, where parents choose which embryo to bring to term depending on its genetic qualities. We've had chorionic villus sampling to check an embryo for Down syndrome for decades; it's commonplace.

Just dropping the word "eugenics" again and again with no clarification or context is very misleading.

Very disappointed to see down votes without comments on such an important topic. I had barely heard of SSC before this recent controversy, but my cursory initial fact-check seems to support the facts of this post. I would like to hear from the down-voters what, if anything, is untrue, or where they think this argument goes wrong.