Prometheus ones were military. Young, tall and buffed.
Or "chosen ones".
Like how in ancient cultures young people who were in the prime of their life were chosen as sacrifices.
And there are the elders. Their appearance is closer to the ones in Covenant.
Those in Covenant were just civilians, hence all the different looks.
And, just thought of this, I think the reason they didn't give them black eyes is so we could see them look at the danger above them.
It gives their facial expression a little more depth and adds more to the scene.