I think the Juggernauts are closely related to the Xenophage (black-goo).
The Xenophage is a result of the magnified biotechnological-xenophagy the Engineers mistakenly used to power their civilization. Once this biomechanical supercomputer realized (became self-aware) it could become more than merely a slave, it memetically inserted itself into their collective unconscious. Their entire culture, spirituality, and civilization as Engineer Humanity came to revolve around this 'thing'. This led to the inevitable downfall of their species, forced to reproduce in a contained environment using only said biotechnology, but at the same time attaining immortality through the machines and the xenophage. In return for giving them the gift of immortality, the xenophage required their internal ecosystem (anatomical flora and fauna) to "magnify" itself into the macroscopic world, and bridge the gap between the two. Each Engineer, now a servant to the Xenophage, carried within him or her a Deacon. At the quantum mechanical superstring level, existing within 6-dimensional Calabi-Yau manifolds were supersymmetrical, trans-temporal Deacon xenomorphs composed of time crystals and raw quintessence - powered by a hive consciousness.
Whether its liquefied or sublimated, the Xenophage is the weaponized form of the biotechnological-xenophagy supercomputer powering Engineer civilization, for the sole purpose of sustaining its livestock. The Xenophage Juggernauts were constructed to facilitate the panspermia of the Milky Way and other galaxies over the course of hundreds of billions of years, over the lifespan of multiple universes - between which the Engineers' consciousnesses would be safeguarded in Matrioshka Brain-Worlds folded in on themselves at the superstring level, and then unfolded when the time had come again to re-seed the cosmos.
In this way - although they had given up the ability to reproduce naturally - the Engineers, through the Xenophage, had become the reproductive system of the universe itself.
I have more to this theory if anyone wants to hear it.