I think it was largely a case of too many cooks, leaving it incoherent. The original script was a decent Alien film, and worked very well as a prequel, even if not especially unique. They had the talentless hack Lindelof re-write it, and at some point demands from the studio or some other higher-up tried to divorce out the prequel aspect while still having it be set in the "past" of the franchise, making it fractured all over the place. When you combine that with Lindelof's inability to write characters intelligently, his love for Mystery Box nonsense, and the multiple levels of rewrites it all went through and apparently Scott's love of vapid philosophizing in his films, I don't think anyone was "trying" anything by the end except to make a movie that looks and sounds like a deep, thoughtful film just enough to fool audiences into thinking it was one.
It wrecks existing worldbuilding, exists as a prequel but doesn't actually act as a prequel, asks questions it has no intention to answer (but presents as though it should), contradicts its character-building with their actions but cannot acknowledge it, and is ultimately not interested enough in being either its own thing or a contributing to the existing franchise. It is, at best, a decent-looking film visually. It wastes every single actor's talents, even Fassbender who is the stand-out doing his best in the least-inconsistently written character present (but even David is a giant mess).
tl;dr - I suspect you were confused by what they were trying to do because there was no coherent, consistent vision on what they were trying to do.
