Its simply a case of changing things as they go along... so we shall have to wait and see what happens between NOW and ALIEN.. however it is looking like David will arrive at Origae-6 which means he will arrive at this world about 10 years prior to the Events of ALIEN and so if those Eggs are Davids Creations, then they have to end up on a Engineer Ship on on LV-426 which we can safely assume is quite some distance from Origae-6 and all this will have to happen within a 10 year timeline.
Sadly it appears they make it up as they go along and dont consider what groundwork was laid before them in previous movies, and any given LORE or Comments and Interviews made on any subject connected to Alien and also this includes Viral/Marketing information that was meant to play as a History/Back Ground.
Nope Nothing is Safe from them simply changing things as they go along...
Initially indeed the object was to show case the Space Jockey as a Ancient Event, and Alien Engineers tried to Shoe-horn it in.. but with FLAWS. Prometheus just gave us vague clues, but we could see there was a connection between Xenomorph and the Experiments that had been conducted on LV-223 and the Outbreak and Space Jockey was likely a connected event.
Ridley Scott even confirmed it... Here is the Final Answer for the Space Jockey prior to Work on the Prometheus Sequels.
*The Space Jockey was a Engineer, well a brother to the Engineers
*The Derelict was a brother to the Juggernaught and Technologically they are a few hundred years apart.
*The Derelict was carrying a Bio-Weapon Cargo
*The Derelict left for a undisclosed location but it did not get FAR.
*Something in the Cargo Hold Evolved and it got to the Pilot.
*Knowing that the Pilot was infected the Space Jockey set down a course to a near by Barron Moon to Quarantine the Cargo.
*The Derelict did not Crash, it was intended to Land where it was found.
*The Space Jockey was Chest Busted during the Final Stages of landing.
*The event had occurred within a Few Hundred years of the LV-223 Outbreak that killed off nearly all those Engineers 2000 years ago.
So in a Nut Shell, the Derelict had THREE Outcomes....
1) A Earlier Model Juggernaught had been transporting a Cargo that Evolved and infected the Pilot who then attempted to Quarantine the Cargo but Crash Landed on LV-426. Many years latter the Engineers recover something and begin Experiments on it on LV-223 the results of which are Stored in the Urns, until the LV-223 Outpost suffers a Outbreak some few Hundred years after the Derelict Crash Landed on LV-426
2) The Derelict was a different model that had loaded some Cargo from LV-223 a few hundred years after the Outbreak, but the Derelict did not get far before the Pilot was Infected and Crash Landed on LV-426
3) The Derelict was part of the Mission 2000 years ago before things went to POT, and the Pilot had attempted to go into Cryo-Sleep to escape the Outbreak.. He had awoken a few hundred years latter only to find that he was infected by something that Evolved in the Cargo Hold and so he then proceeded to continue his mission but he only got as far as LV-426 before he had to Quarantine his Cargo and Crash Land on LV-426
I would say all Clues point to OPTION 3 being the most likely
As far as Space Jockey Size... Indeed the Space Jockey would have been 13-15ft tall, and indeed the idea for the Prequels was that the Space Jockey Engineer Race would be 15ft Tall, this ended up being 12ft for Prometheus Drafts... but the Final Product we was to assume are 9-10ft tall..
Sadly the Illusion did not work and our Engineers only appeared to be 8ft Tall Maximum, similar Scale Problems also happened with AC, where the Engineers Ranged from 6-7.5ft tall.