So let me get this straight

round flying saucer ships = life givng benevolence horseshoe shaped ships = life taking military vessels of doom

The Engineers seeded life on Earth by sacrificing one of their own. We are not made of the black liquid, the black liquid was simply used to sacrifice the Engineer, it broke down his DNA, then reconstituted it into new DNA strands, which led to multi-cellular organisms, and eventually, humans. Engineer DNA and Human DNA is a 99% match. The ship is the opening scene does look different, but it is never explained why. Maybe it looks different because it serves a different purpose than the Derelict ships. Or maybe it is the ship that the Elder Engineers use. Who knows?

The first scene takes place almost 4 billion years before the scenes on LV-223. I'm sure whatever we're flying in 4 billion years if humans last that long won't look much like the Apollo lander, either.