Not that the prior 4 alien films (I'm ignoring AVP for now) aten't problematic but didn't need a rational backstory. Item: soon after the original alien came out, I'm in a bar with my coding geek coworkers and we got to talking about the weird Alien movie and the convoluted way the alien reproduced. I pointed out that parasitism is a vast and highly lucrative evoluionary niche, but the way the facehugger huged faces would suggest design. Too specific of a vector, and Ridley Scott confirmed that aliens are designed.. These things are bioweapons. Multiply that in the movie Aliens .
The Alien franchise also inhabits the same universe as Bladerunner (and a 1998 Kurt Russell movie called Soldier} with replicants of those films being organic and eventually synthetic like Ash, Bishop, David and Walter and Call. This connection to Bladerunner/Soldier confirmed that humans had FTL transport, massive (fusion?) power generation to move gigantic shit around the stars. The other commonality is artificial general intelligence, which is far huger than mere fusion power. You see, once you have such a substrate, like a Universal Turing machine, you can run any conscious software that you like, human or alien. Couple it to a material insturmentality and you have protean technology. The only thing scarier is giving this access to life forms, input and output tailored for whatever by what looks like a black goo. (Per Sir Ridley, the black goo can only infect animal forms not plant. Its a rationalization to keep the human protagonists being eaten alive by the grass itself when they set off the lander).
So the black goo is the real villain here. Eating everything in its path to satisfy its objective function. In all the movies, there is no will or intent from this stuff except to spread. David, the android from the 2 prequel movies, is the designer of the xenomorph, but he is using another being's workshop and tools (the Engineers).
Alien Covnenant is a glorious mess, but it solidifies where the prequels end and the first Alien begins.
What is harder to explain is that humans (per Prometheus) are engineered. In that movie, we see the replicant version of the Engineer species, the Space Jockeys, giants 8 to 14 feet tall. They are not androids, but biological replicants just like Decker and Kurt Russell's character in Soldier. (The story of Soldier is how the synthetics were favored by the corporation over "obsolete" replicant soldiers)
As biological replicants, and unlike synthetics, they are vulnerable to the black goo, which is why the planets in Prometheus or Covenant are not the Engineer home or colony worlds. They were military bases. Go back and look at the Covenant footage when the Juggernaut docks and before David bombs them all with goo, they have the look of soldiers and airmen at Tinian welcoming back the Enola Gay from bombing Hiroshima. And then the goo hits the fans.
The alien world in Prometheus was both Area 51 and a strike base for the Engineer race, clearly. The hubris of humans to waltz in was well depicted, arrogant stupid little monkeys.
In the confrontation scene between awakened Space Jockey and Weyland, Sir Ridley tells us David asked the alien "This man wants to know if he can have more life". The Space Jockey carresses David's hair, and then picks him up and rips his head off. The Space Jockey is enraged because their black goo weapon had sent back dolls. What the fuck am I going to do with these things as ground troops? Cancel the whole batch.
Can you blame the guy? We were supposed to be super weapons like the xenomorphs.
Where does this leave us? The first and last question of this whole film series is why the goo? Who is the Eneny that so frightens them they create this doomsday goo? I can't see it being a rival facion of their own species. At this point you can throw in the AVP universe and suppose the Predators are their enemy but I think not.
There's something scary out there, if you think about it. Way scarier than jump scare monsters. In future Alien movies, here are known facts.
1 David is still alive and has a planetary laboratory on Origa 4 or whatever.
2 The Engineers are out there and they are still at war with some Enemy.
3 The Enemy is out there as well
4 Earth is a legitimate target to the section 51 crowd.