It's true that it's legal geographic size is ~1.5 square miles. However if you look at Google Maps a good 30% of it is just empty/undeveloped land previously (still?) owned by the military.

So yes, it's still bigger geographically, but it still only takes 15-20 minutes to walk from one end to the other; I've visited a few times. I'm not very familiar with either location you mentioned, but I would say for Marfa to be 3 hours away from the next-largest town (El Paso), have no commercial airport or passenger train line, and still be a self-sustaining walkable town is impressive.

I'm possibly mistaken, but the first example you pointed out looks to be an apartment complex next to a train station within a larger city and Hercules, CA is a 20 square mile (maybe I'm looking at the wrong city?) suburb of SF; I don't think those are examples of what this article is saying?