what I could make of it was that we evolved into being very similar to them

Unfortunately, the movie is very explicit that the alien DNA is a "100% Match" to the human genome. Further, other dialogue then takes this somehow as evidence that we should "throw 300 years of Darwinism out the window", as if evolutionary theory could be overturned by merely some paradoxical results from alien DNA.

In the beginning, it's as if the Engineer had been de-evolved so that life could evolve on Earth

Yes, ok...and then we had nothing but microbes for 3 billion years...but whatever...

Maybe they expected us to evolve into something else?

In fact, we would have evolved into "something else". There is no way that even if we look/act/think like aliens that our DNA sequence would have evolved so such that ours converges to theirs in a "100% match".

(Evolution is random and the human genome is rife with inefficiencies, mistakes, and Rube Goldberg mechanisms, and there is far more than one way to specify a human.)

No offense but I think you missed the point: which was basically to set up a false dichotomy between ancient Bronze Age pastoralist religion and modern science, and decides on a third way of woo-woo intelligent design by inscrutable creators.

which is consistent with this quote by Ridley Scott: "NASA and the Vatican agree that is almost mathematically impossible that we can be where we are today without there being a little help along the way"...