The engineers make no sense.

That's not Earth in the opening scene. The fact they look the same could be because they can manipulate biological forms. They may even be clones. They're evolution may be stunted by their technology. Really an endless list of reasons why. But the fact they are still kicking around is a huge disappointment. Would have been better for the story that they were wiped out by their arrogance.

Truth is we do not know much.

In a universe of 13 billion years, the 4 billion years is certainly not trivial. However, perhaps they are from another universe? perhaps they have evolved to a perfect stage in the first 9 billion years... it is impossible to say. But is it relevant?

What we do know is that the Engineers started life on Earth and continued to visit Earth as we evolved and developed. It seems to indicate they sort of engineered the universe(s) with numerous planets in their petri-dish. Like investments, it takes years before it is time to revisit and reevaluate… This is just what they do.

Next thing we know is that they have outposts of military purpose. And they have farming type societies of primitive living.... what does that mean? We do not know.

IMO the story of Prometheus and Covenant tells their story as a once grand race "populating" the universe. They are a race of tradition and holds religious aspects (monk type culture). At one point their civilization doomed themselves when they developed the black goo for the purpose of destroying life instead of creating it. Was this when they changed from a monk type cloture to a military type culture? When we enter the picture, they are gone. The planet we see in Covenant is their last sad remains of primitive worshiping culture. Effectively ended by David. So, like the Romans, they rose in prosper, concurred and fell.

Did this take them 13 billion years? 5 billion years? We do not know. But is it a far stretch that a dominant time of their existence/history was in perfect balance, peace and harmony before it went sour…. I do not think so.

Maybe at some point, you wise up and go back to the old? I'd like to think an advance society can also teleport, at least locally on their planet. So cars are gone! Trains, planes, all gone. No corporations branding or trend setting? So wearing what feels most comfortable like robes and slippers. LOL! Maybe that's what a species free of superficiality looks like. Maybe that's why they changed their minds, they saw a Katy Perry music video.