That's a pretty ridiculous list of US places to try to argue against SF being dense for the US. Not all of them are as absurd as the 362 people near Louisville, KY, bit, but basically that list says "NYC is denser than SF, as are a few relatively small parts of LA, but SF is easily the second densest large city in the US."
I agree, the US list is skewed by the effects of county size. However, the 5 boroughs of NYC are geographically large in a human scale. All of them are more densely populated than San Francisco, including the ostensibly suburban Staten Island.
Meanwhile, Tokyo is vast and, until recently, could not have Manhattan-esque skyscrapers. It is substantially more densely populated.
San Francisco is more densely populated than a suburb. But the idea that it's amongst the most densely populated places is just not true, either in the world at large or the USA in particular.
