However RS had been quized over the Bio-Mechanical Xenomorph and in regards to the movie he did prior say the Xenomorph felt Bio-Mechanical and a Weapon and Alien Covenant they will explore how this came to be.
After AC we have seen RS come out and mention that we are not quite there yet as far as the Original Bio-Mechanical Aesthetic and so i think by the time RS has finished his prequels then the Xenomorph will be more closer to the Original and for sure different to the one in Alien Covenant.
Which is where the OT Points come in very handy...
1) Indeed if we assume Davids creation was via various experiments and cross breeding but needed Dr Shaws Egg Cells, then maybe we have yet to see a Birthed Finish Product (The Xenomorph's in AC) go on to Procreate, i am sure RS is not going to show us the Organism can not procreate and that the only route to them is using experiments on a Female Humanoids Eggs.... and so yes if Davids AC Xenomorphs lead to a Procreation by Egg Morph, a Queen or some other method those Alien Covenant Type Xenomorphs Procreate then yes maybe the Off Spring to those could become more like the Original.
I however would think they would logically become the same as the AC ones or less Bio-Mechanical. And so would prefer some other route.
3) Indeed we see the Engineer on LV-223 Suits are connected to the Engineers as if they are part of his Body, and they do have a similar look to the Xenomorph, slightly and indeed their Space Jockey Suits seem to connect to these Pressure Suits and if the Space Jockey Suits are some kind of Bio-Technology where they are a Fusion of Synthetic and Organic Material.
Then indeed a Xenomorph birthed from a Space Suited Engineer could maybe take on traits from his Bio-Mechanical Suit.
But the only way this would lead to the 1979 Xenomorph would be further experiments based of this Ultramorph to incorporate its new Evolved Genetics into those Eggs... or the Ultramorphs Procreation leads to those Eggs.
2) I cant see how David can mix his DNA because he has none as he is Synthetic, but thats Nit Picking... i did think prior to Prometheus that this movie would Show David Evolves himself into something more than a Robot... i.e he becomes more a Real Boy and so like Pinocchio and this however had a cost as he could become infected by a Face Hugger or the Black Goo.
This was not the case though... but The Fire and Stone Comics introduced us to Elden a Synthetic Construct who was part Synthetic/Organic and he was infected with the Black Goo... so maybe a Synthetic Construct could be infected with a Face Hugger?
The Walter Viral site does seem to tease that Walter could have some kind of Synthetic Organic Qualities to him, or maybe they just decided that as well as looking Human on the Outside, Weyland-Yutani decided the internal components of their Synthetics should somewhat resemble Organic Human Parts.
If However Walter is part Organic then Walter or another Walter model, or a David using Walter Parts from the Covenant could provide a Route to show us how the Xenomorph gets its Bio-Mechanical Look from... and then this resulting Xenomorphs Procreation or experiments on it lead to the Xenomorph in Alien but again all those Eggs have to carry this Evolution.
I can offer another explanation....
The Black Goo can be programed and modified and so maybe a modified variant can infect a Synthetic Advanced Walter, or if not... then i propose this.
At some point the Eggs get loaded onto the Ship, and one of its Cargo Holds has Black Goo, and the Ship Crashes due to the pilot getting infected.
The Crash Landed Ship, then Spills out its Black Goo that somehow reacts with the Eggs and a a Freak Evolutionary event happens where this Black Goo mixes with the Egg DNA and this substance then infects the Ship, which leads to the Ship Evolving and taking on DNA from the Eggs, while where the Eggs where they then Evolve into Eggs that take on Synthetic Traits of the Ship.
Thus the Crash causes the Organic Eggs and Mechanical somewhat ships to Merge Genetically.
some of the infected material spills out onto the surface of LV-426 and starts to grow some Bio-Mechanical features on LV-426 and explains some of the same Bio-Mechanical Piping that is found on LV-426 not far from outside the Derelict, but also matches a lot of the interior of the Derelict and the Pipes etc on the Xenomorph.
This would be the Route i would go to explain the Aesthetic Difference.