If the city was buried, the arch would be buried with it.
The arch is not buried, ergo the city is not buried.
The city is gone because St. Louis is the gateway to the West. Which is metaphorically what the arch is, a literalization of the notion of a gate to the West.
In one sense, Defiance is setting itself up as an SF alternative to the real history of the country. Instead of a genocidal war, racial tolerance. In principle, democratic governance could be part of the package. But the show seems to want to stick with the Strong Man motif of so many Westerns. By literalizing the different races as genuinely alien, the show risks (or wants?) raising genocide as a moral choice worthy of serious consideration.
Nolan's relationship with the girl would have pedophile overtones if she didn't seem like a hard, high-mileage adventuress in her mid-twenties.