Anyway i am going to go answers some stuff....
I cant say where and how the Xeno came about.... only that if i use Gigers Mural for Prometheus it gives us a clue to something more connected to Star Beast inc ritual purpose of the movie, where Star Beast and Giger Xeno Life Cycle seemed to indicate in the race that we now know as Engineers Ritually Sacrificed themselves to produce Xenos...
Did they create us, because there numbers was small and so why Sacrefice themselves when they could create a race in their image to become the Sacrefice...
Star Beast showed us these Engineers well the beings in Star Beast did not create the Xeno, they came across some ancient organism and due to the nature of its life cycle for some reason they worshiped this cycle and they used the temple they found to perform sacrificed to the organism..
Why? we never know...
These beings then was trying to carry the leathery urns to their ship when they got infected by the Octpoid Face Hugers.
Now Prometheus Mural again shows some Ritual significance to the Deacon/Xeno Organism in the Mural, and we see what looks like a cross between a Face Huger and Shaws Baby that is Face Hugging a Engineer, this appears twice as mirrored image.
This looks like Shaws baby when it was young but also like a Face Huger but the fully grown Shaws Baby Trillobite actually looked identical to Main Mural Image of the Organism in the Temple of Star Beast yet the end result in Star Beast is described different to what is seen in the Mural.
Likewise the Deacon in the Mural looks different to Xeno and more like the Deacon at the end of the movie.
Now we cant use Star Beast as Canon, but even so Prometheus either shows us a depiction of events to come... i.e prophecy.
Or its shows us events from a past that these Engineers worshiped for some reason, if thats the case then we have to ask does it show the Deacon as the end and desired result? does it show they either Worshiped something that one time came from a Engineer who got Face Hugged by some Face Hugger/Squid like creature.
Or is the Deacon the Ancestor of these creatures... we cant be sure but i would say the prior.
This is just a stab at how and why the connection to the Xeno and Engineer and their ancestors...
Now if we move on and look at the Derelict and Eggs, and for this we can take Aliens as Canon and i dont mean the Queen although i am not throwing it out as i do like the Queen...
What i means is watch how Xenos acted in Aliens, they was controlled by the Queen, by some kind of Hive Telepathy, basically the Queen may be able to remote control and give orders to the drones...
Back to Prometheus the one Fresco that we never saw fully as it was part breaking down... but images are around of the full image and it shows a traditional Xeno hand... (not Deacon) holding a tradition Xeno Egg...
There is your answer..... A Xeno can carry a Egg maybe without setting them off....
How did Engineers get Eggs into Cargo Hold? Maybe they somehow could control the Xenos to get them to carry and load the Eggs...
But they can not control Face Hugers....
And on LV 223 it was a outbreak of the stuff in the Urns and not Eggs that got to those Engineers, so maybe they experimented with the Xeno Genome and Eggs to create the Goo as a safer way to store and transport as they had difficulty transporting Xeno Eggs by Hand or they had to use Xenos to do that, and for some reason they had a way to manipulate and control the Xeno but could at times lose control.
Hense re weaponized Goo but as the found out, spill that stuff and you in a pile of poop..
For the above i never used some stuff to base it off, such as Star Beast and others.. or never mind Gigers concept which clearly showed the Derelict/Juggernaut i.e Space Jockey Craft was actually more Biological than we know and it actually was a flying Egg Making Facility.
As far as the Hammerpede goes, well yes laying Eggs could be a good idea, and we dont see what became of Milburns body so we could assume that Eggs are laid inside that will feed on Milburn when Hatch.
I would knot now how such Eggs could evolve to grow large that way, only if they are laid on the floor and maybe the goo mutates them, but we have to assume once the substance as mixed what ever DNA it carries with a Organism that Organism while it can Evolve it cant be radically mutated twice...
But then thats not to say it could happen...
Also as far as using the Hammerpede or Deacon to be a progenitor to the Xeno, i think clues and comments around suggest the Xeno Eggs on LV 426 had been around at least thousands of years before the events of Prometheus.
R.I.P Sox 01/01/2006 - 11/10/2017