> "Your children aren't just dumber, they're also poorer" feels like a very spicy way to elevate the status of a state to me.

Would this comment have been made if we were talking about The Bronx instead of Mississippi?

The author is saying that given the poverty status of the state it's remarkable how quickly they've been able to turn their education system around. A really good school in The Bronx will have lower scores than a mediocre school in Upper Manhattan, but that doesn't mean that we should all go out and emulate the mediocre school in Upper Manhattan. The really good school in The Bronx is obviously the better model.

The author's initial point is correct, though: because it's Mississippi we're talking about that intuition doesn't apply. It's okay to diss on Mississippi for being Mississippi.