Alien Covenant appears to be ever changing and evolving as a production, i would think alot of this is probably down to Scott and Fox both seeing many different script iterations, then incorporating and carrying forward aspects of these scripts they liked to form the finalised
screenplay.One thing Prometheus did, was divide opinion amongst its audience and the studio will look at, what worked about it and what didn't. Prometheus performed reasonably well at the box office, but it had faults in script, character writing alongside pacing.and fox know people want another Alien movie, but we want something which evokes the quality of the first two movies. With Neil Blomkamps recent movies not performing particularly well and the mixed opinions of bringing Ripley, Hicks and Newt back into the franchise by ignoring everything after Aliens is a risk.Maybe fox saw Ridley coming hot off the success of the martian and is much more bankable than Blomkamp at present. Fox know a new Alien film with Scott directing is going to have audiences queueing up to watch it and going back to explain the aliens origin is potentially safer than making a new aliens sequel by Neil Blomkamp, which disregards Alien 3 onwards.Scott likes each of his films to be unique in story alongside visuals and with a new trilogy, they can potentially achieve that. That way we leave the whole franchise, as it is chronologically intact, explore the aliens origins and introduce new characters. If shaw is not in the film and what happens to her is eluded to, but not in detail, it can be explored in a sequel or in a separate film, if that's what they choose to do with her character, this way everything to do with prometheus and the alien movies remains intact, plus Scott gets more freedom to explore a new franchise, with new ideas.If we don't see any engineers in alien covenant, they may hold that back and explore it, in a separate film following shaws character arc, or they may just directly kill her off in alien covenant. Either way alot is happening, it's exciting, but also confusing, all we can do is speculate and debate for now.