First, you quote her as stating: "the Wuhan lab did not have "the fucking virus" -- we don't know what they had or did not have, because the Chinese government is not exactly being forthright on the matter." But her actual tweet notes "To have the virus originate at the lab under any circumstances, the lab has to have the fucking virus!" That seems to be a logical conclusion, which your framing dismisses.
Rasmussen continues by stating "Not only did they not have intact, infectious, replication competent RaTG13–which, again, is not SARS-CoV-2–at WIV, there’s no evidence they had any ancestral proto-SC2 virus." The first point was explained by the tweets above that one, and the second point is clear. There is no evidence that they had the virus, so any argument that there was a lab leak requires them to have the virus in the first place, going back to her first axiom at the beginning of the tweet.
But the bigger issue here seems to be one of framing. Yglesias frames the preprint in the context of the press response to it, and not so much the actual contents. The abstract clearly states: "Together, these analyses provide dispositive evidence for the emergence of SARS-CoV-2 via the live wildlife trade and identify the Huanan market as the unambiguous epicenter of the COVID-19 pandemic." Note the lack of any mention of a lab leak here, or anywhere else in the preprint. Rasmussen's rebuttal is done in the frame of the conclusions of her research, which Yglesias misinterprets as a paper trying to disprove the lab leak theory.
Considering that he cites those figures as from the New York Times instead of from the appendix of the preprint, it seems pretty clear that Yglesias is responding to the New York Times article and probably didn't even read the actual preprint.