There's always the chance that this particular city was their Vatican or Mecca and could've been located in an extremely isolated part of the planet.
Remember that planets are huge, and as big as our cities are, you can be somewhere on Earth with not a single city in sight. It's possible that there were other Engineer cities but we just didn't see them.
The Black Goo likely dispersed into the atmosphere and became an airborne virus that spread as far as it could, with infected animals and spores finishing off any Engineer survivors, Plague Inc style.
Also just because the Engineers are basically humans doesn't necessarily mean that they developed exactly as we did. For all we know, they could've taken their environment seriously and kept their populations balanced with their world as opposed to having 10 billion big bald dudes walking on its surface and leeching its resources rapidly. Maybe they didn't even build massive cities because they had no need to.
Who knows why they even went to space? Did they have their own America-Russia space race? Or was it driven by curiosity or religions reasons? Did they have environmental pressure to leave their world and colonise the stars as we humans do in the 22nd century? Or was it for the sake of discovery, exploration and species wide achievement?
We know they were a very ritualistic and religious people, like us, but their beliefs have steered their society in a different direction. We don't
Spoiler
sacrifice ourselves to birth Xenomorphic monsters for the sake of cleansing ourselves of our sins.