They are just so different though. The Alien from the first and second movie are very different thematically and even abit aesthetically.
In the first movie it is a "perfect organism", requiring no hierarchy or other social systems to function and reproduce. The egg was a stage in the Alien's development and wasn't laid, which you can see in the deleted scene in the first movie. The Alien was supposed to be extremely different from what we know from our world.
The second movie made the aliens much less alien by making them ants/bees and by explaining everything about them in very simple terms. Which turned the perfect organism into cannon fodder for the main characters.
I don't like Prometheus or Covenant at all but I do very much enjoy Scott's themes in the first movie and I understand his frustration with Aliens.
Except Ash's assertion of the Alien being the perfect organism is not related to being self contained, as is explained by the Writer Dan O'Bannon and actor Ian Holm, it's the perspective of an android frustrated by his own lack of true life, seeing a creature that is biomechanical, a blending of his own limited existence with that of his organic creators, but surpassing both not only physically, but without any of the restraints of either his programing or human notions of morality, fear or greed.
As ash says "I admire it's purity... A survivor... unclouded by conscience, remorse, or delusions of morality."
The 'egg morphing' scene is also not an intended implication of what is happening within the nest Ripley finds. Both Scott and O'bannon have stated that that is not what is happening to Brett there, and infact it was this scene that was the inspiration for the hive in Aliens, expanded upon alongside all the many details and production notes from the first movie talking about how the Alien design and life cycle is explicitly insecr like, specifically taken from parasitic wasps that lay eggs on or in living hosts.
The original life cycle for the Alien was intended to have been that of an intelligent species evolved from such parasitic insect like life, with the Space Jockey having discovered one of that lost civilisations great pyramids, housing their eggs, awaiting hosts. This pyramid was cut and the eggs added to the Derelict only due to budget constraints and run time concerns. The idea that the eggs are an Engineer bio weapon, lining the inside of the ship like bombs to be dropped on an unsuspecting population, is a a fan theory that Scott adopted well after Aliens, and was also never intended to have been either the origin of the species, nor even a tie between the Aliens and the Space Jockeys.
Now if we want to talk about themes, then the real them of Alien is sex, sexual violence, disease and birth, all of which are motifs repeated through Aliens and again, expanded upon, specifically to include motherhood, and the survivors guilt and trauma of sexual abuse.
There's also the theme of average Joe's suffering through the extraordinary that is present in both films. The protagonists are blue collar, working class folk, Space truckers in the first movie, and construction workers and soldiers in the second. In both movies the white collar, middle class, corporate higher ups are as much the villains as the Aliens themselves.
The alterations to the design of the Alien between the movies is also not the travesty people accuse it of being, and is in reality a refinement of the design and closer to the original intention that was unable to be realised at the time.
The most obvious alteration is the head design, but this is primarily a removal of the clear dome of the Big Chap, specifically because you were meant to be able to see all those details, but due to the weakness of the costume and unfortunate need to paint it mostly black (it was originally all clear, but when it came to film the actor within was too obvious and the materials used too prone to breaking), obscuring the internal structures. The Aliens design is once again closer to the original intended vision for the creatures, but with Cameron's superior understanding of special effects being able to better bring that vision to the screen, while also making costumes that didn't fall apart halfway through filming (the Big Chap suit was almost completely destroyed while filming the Narcisssus sequence, and had been having bits fall off, crack of break since day one of filming).
Now, if we're talking about retcons and fan theories, as the egg morphing was, then that is precisely what all of Prometheus and Covenant were full of.
Scott so spectacularly got everything wrong about Alien, it's themes, it's popularity and it's intended story, that he actively undermined his own work by retconing the Space Jockeys to the Engineers, making them vastly smaller and no longer symbiotic to their technology, as they had been intended to be by O'bannon and Giger, made them both the creators of humanity out of nowhere and undermined the 'perfect organism' nature of the Aliens, by making them an accident of the black goo combined with the inferior tinkering of the mad android David.
And even then, the likely now cancelled Alien Awakening, the sequel to Covenant, was meant to show David creating the first Queen, so not even Scott himself found the furthering of the insect analogies to be inappropriate.
So no, I reject your premise of the two movies being incompatible or thematically incongruous. There is far more similar between the two than different, and most of what you're reading into the first movie is either unintended and unsupported fan theories or retcons brought about by Scott, who showed less respect and understanding of Alien than Cameron did.
Alien does hold up as a singular, stand alone work in a way that Aliens cannot, I will grant you, but the two stories combined show an almost unheard of consistency and completeness as a narrative, that I would argue no other unplanned movie sequel manages, beyond maybe Terminator 1 and 2, and even those had the advantage of a consistent, singular vision behind it.
