SquarePizza,
Question 1 has also been towards the top of my theoretical concern list as well.
Ridley did a rather crap job of completely bypassing all the potential explaining of the engineers, simply kill 'em all - must had sounded good to someone...
Question 2, also very troublesome considering the context now given. The other lurking question is where did the Alien Queen come to be in all this.
In the AvP universe, I think it was the first film that said the Preds brought technology and blah blah blah to Earth, but every 100 years or something they needed a 'sacrifice' which mean a Xeno hunting spree beginning from face huggers. It's like a 30 second scene in one of the movies...that I remember
I know the tentative plan was for the sequel to Covenant to hit production in like 18 months or less following its release, and that would tie directly into the original 1979 Alien, supposedly tying everything together.
However, with the rather mediocre performance financially of Covenant, I have a feeling Fox is gonna put the series back in the freezer or cut out Ridley if we're even lucky enough to get a second from here. Which is a shame, because I love the films and whole series, but it's may like Resurrection and now have to wait another decade for a new one...