At the end of Prometheus, Dr. Shaw say, that she want to go where they come from, not to their homeworld. There was not mentioned even one word about something as their direct homeworld. Only in deleted scenes she say, that she want to go to paradise (who not) So, it is evident that planet where Covenant take place is another terraformed colony where is another race created by Engineers.
If the Engineers could create the Humans, then they can also create another different species. These humanoids are not Engineers, maybe that they have similar clothes like the elder Engineers from deleted scenes at the beginning of Prometheus, yes they have bald heads, but that does not make them Engineers. We see that these humanoids live in city that is different in the terms of design and architecture than anything that is connected to the true Engineers.
There are only some statues, in Citadel wee have the sculpture heads of the elder Engineers. In the center of the plaza we have similar landing ground like we see at the end of Prometheus.
And that is all, of course that in the whole movie we could see much more, but at this point, we can clearly see that these humanoids are almost like us, intelligent and organized.
I think that wee see mostly the parts of their own structures with only the small combination of some original aspects that Engineers have.
It seems that long time ago, Engineers leave them, and let them alone. Maybe that is the reason why they want to meet their own creators once again (in the case that they really know who created them).
I guess, they are thinking this is just another visitation, it is very important for them. They come to see it at their own eyes, even the landing ground opens for the Juggernaut ship. Later in the movie, we see that exact langing ground fully open.
And what about this new "Scorpion" ship? Is it the ship of the these humanoids? I dont think so.
Because if this is their ship, then some of them can survive the whole disaster. I dont know what to think about it, but it seems this "scorpion" ship could even attack the Juggernaut with David and Dr. Shaw on board. Perhaps this ship is there to defend the entire city, who know? Juggernaut ship crash-landed somewhere in the forests, this could mean that once the David start killing these humanoids, "scorpion" ship could respond on that with shooting. It should be logical.
If you remember the beginning of Prometheus, there was a huge circle-shaped ship. Once the Engineer drink the black goo, the ship flew away. Remember the movement of the ship moments before it leaves the planet? that ship flew straight-up. This "scorpion" ship here is standing similar like the circle-shaped ship once it leaving the planet, thats no coincidence.
I apologize for my English, Im from Czech Republic, Europe. English is not my language.
Thanks for reading this! Im waiting for this movie since the end of Prometheus. I love both Alien and Predator movies.