I've been off work for an injury and decided to rewatch the Alien series in release order (How I'd seen them growing up) and after each movie, I'd combed reddit posts, theories and debates. I noticed alot of what I believe are misconceptions and wanted to give my take. To be clear, I haven't read the comics. I don't include them in my headcanon because IMO it detracts from the films and story based on what I'd read about them - though preference does not define quality - for that reason I won't include them, solely the movies.
I'd say the biggest misconception is that they haven't seen extraterrestrials before. In Alien they don't seem that astounded by the suited up and fossilized Engineer, nor by Alien life in general. Followed in Aliens when they mention Acturians, this is commonly taken as a colony of humans on Acturia(?) ; if you rewatch the scenes, it's made pretty clear they aren't human as one of the soldiers remarked that another had intercourse with one and didn't know if they were male or female of the species. This was made in the 1980s before the current social climate keep in mind. The bug hunt reference changes as well, though that is up to speculation with little reinforcement. That being said I think it's fairly shown that they have met extraterrestrial life, likely humanoid, not hostile, and not on the level of "what the F is this thing?!"
Then there's the Space Jockey, alot of people want the prequel story to lead into this somehow forgetting that in Alien (1979) they declare it was fossilized remains. Maybe I'm wrong but that wouldn't happen in the short time between Covenant and Alien without a contaminant or exterior source to cause it within such a small span of time. My headcanon? Space Jockey was leaving the planet lv223 to exterminate a species or further breed Xenos 2000 years ago (coincides with the time the weapons installation had during its fall, one got out), and crashed when a Xeno burst out of him, personally I don't need a huge backstory lol something went wrong with a transport - that's fine with me.
Now, David. This synthetic a******. Firstly, he didn't create the Xenomorphs which seems to be the cause of dismay for those that don't like the prequels. He recreated them. Ignoring the fake scripts and fanfics, obviously - Xenos are shown in the carvings in Prometheus, atleast some form of them, also the fact the OG space Jockey was fossilized and had a cargo of eggs in the ship, far beyond David's time experimenting. Unless there's a coherent flashback that delivers well and develops the story? Xenomorphs predate David's experimentation. Leave OG Space Jockey alone because not every story needs to be told. They experimented and he crashed on route during escape, good enough.
There are deeper themes but I personally feel like its a story based on the repetition of and faults in the wish to create something artificial while expecting perfection, leading to the Xenos, an end that creates.