-What direct falsehood is being asserted by Scott's detractors? I don't think anyone is claiming that, say, Scott identifies as alt-right (not even privately), any more than anyone is claiming that trans women have two X chromosomes. Sneer Club has been pretty explicit in their criticism (examples: 1 2) that the Culture War thread harbors racists (&c.) and possibly that Scott himself is a secret racist, with respect to a definition of racism that includes the belief that there are genetically-mediated population differences in the distribution of socially-relevant traits and that this probably has decision-relevant consequences should be discussable somewhere.
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-And this is just correct: e.g., "The Atomic Bomb Considered As Hungarian High School Science Fair Project" favorably cites Cochran et al.'s genetic theory of Ashkenazi achievement as "really compelling." Scott is almost certainly "guilty" of the category-membership that the speech against him is meant to convey—it's just that Sneer Club got to choose the category. The correct response to the existence of a machine-learning classifer that returns positive on both Scott Alexander and Richard Spencer is not that the classifier is "lying" (what would that even mean?), but that the classifier is not very useful for understanding Scott Alexander's effects on the world.
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-Of course, Scott is great and we should defend him from the bastards trying to ruin his reputation, and it's plausible that the most politically convenient way to do that is to pound the table and call them lying sociopaths rather than engaging with the substance of their claims, much as how someone being tried under an unjust law might dishonestly plead "Not guilty" to save their own skin rather than tell the whole truth and hope for jury nullification.
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-But political convenience comes at a dire cost to our common interest! There's a proverb you once failed to Google, which runs something like, "Once someone is known to be a liar, you might as well listen to the whistling of the wind."