Watched your edit and can say it's the best fan edit of Covenant to date. Very well done with the additions that were intelligent & increased my enjoyment of the film, noted improved light, excellent use of soundtrack & the 'Life' track from Prometheus.
Plus You also did a very good job with integrating The Crossing into the Motion Picture.
My humble suggestions to tweak though would be:
Shifting Advent to between David's last scene & 'Walter's' Final report & end credits. I think it's info is lost post credits
Add a couple more snippets of 'Meet Walter' (Funny how the room of both Weyland/David scene & aforementioned are the same) if possible
Last Supper ain't my favourite thing but I think that by adding it the characters get a bit more depth & love in terms of reinforcing an epic feeling that your cut I feel is definitely working towards in a very good way with what you've done already. It just feels as a home for all the major extras made like Prometheus Workprint does, it needs this
Finally I think a little bit of Phobos also wouldn't hurt perhaps, understand as a whole it's trickiness but thought shock flashbacks interspersed with Last supper or simply a flashback of one of the characters later in the movie(Oram perhaps) during a stressful moment would be freaky.
But regardless..even though I'd probably pay cash for you to add those tweaks somehow, congratulations on a great job, thank you and happy Christmas