Massive plot hole or did I miss something?

My explanations would also explain why those Engineers/beings did not seem to be fearful of the Juggernaught.

I would assume a Higher Race/Hiearchy use these beings for Sacrifices just like the Sacrificial Scene but over time they developed a better way to Seed Worlds.

Engineer Dropped off drinks Sacrificial Goo = Broken down DNA that imprints/evolves basic Life.

Overtime maybe the beings above the Engineers or Hierarchy of the Engineers had developed a new way to Seed Engineer DNA.  They would Sacrifice a Number of Engineers and collect the Engineers broken down Material and Store them into Urns.

The Hierarchy/Engineers then just have to fly to worlds and drop the Engineer DNA Cargo onto a World, instead of stepping Foot onto the World and Sacrifice themselves.

This is a more efficient method...  It also would explain why these Engineers/Beings on Paradise/Planet 4 lack much Technology and seem to be Ritual Based....  They are involved in Ritual Sacrifices that is deemed a Great Honor for those Chosen for this Purpose.

RS had explained similar to this for the Sacrificial Scene when Prometheus came out.... This all fits with the Hanger on Paradise/Planet 4 and the Engineers Reaction.

They felt their Hierarchy was coming back to collect Sacrifices, in return these beings are given this world to Live on and are taught things by the Hierarchy/Elders.  In return they Worship the Elders/Hierarchy and also Sacrifice themselves for the greater cause from time to time.

The Hanger had Statues around them that was similar to the Buddha Offering Statues... and thus i think this image fits in and explains what i am trying to get across.

My theory:

The Black goo is a mutant but the Vase is not designed to act as a mutant. There are green ampules inside the vase and it contains a different and transparent liquid.

When the vases are deployed, both liquid mixes and atomizes a swarm of nano-particles in the air which then rips/burns all non-botanical life forms upon contact.

The left over of the original pathogen (the black goo) mutates certain life-forms into something which preserves parasites (such as spore producing pods & facehugger eggs).

This way, if there are any lifeforms that survived the bombing, could eventually get killed by the parasite attack & the resultant 'Morphs which shall prowl the planet.

The bombing scene took place to quickly to see what was going on, but I think I saw and other people commented on, black creatures bursting out of the engineers who were dying.

But I'd imagine the black goo is supposed to be dispersed over an entire planet, rather than in a single area like that, so it probably had unintended side effects lol

The real black goo:

Actually DJ, its Vegemite...... lol. I guess I'm liking your theory Foxcatcher and it fits the story arch. Thanks Big Dave for yyour thoughts. 

I think I have figured out the issue. Ridley now makes many films at a time. When he made Alien his entire creative self busted it's ass to make it the masterpiece we all agree that it is. If only he'd stuck with the original script for Prometheus. Reminds me of Alien 3 and what could have been if the breathtakingly original was allowed to have been allowed to have come to fruition. Alas. 

The Engineers thought they knew what the black goo did, and painted themselves into a corner of the temple/juggernaut within Prometheus. 

Ridley Scott also created the black goo, thought he knew what it did, and painted himself into a corner of Prometheus. 

All jokes aside I do think the path he is taking is more interesting than the original script of Prometheus with no Weyland on board, eggs instead of urns, and the last Engineer being infected and landing on LV 426. I love every bit of the Engineer Lore. I would watch an entire film full of their discovery, mockumentary style if someone created it. Similar to National Geographic exploring pyramids. That won't happen, but maybe if I ever have a few million laying around I'll create it and nobody will watch it, lol.  

Thanks to all the participants of this forum, you are all great. 

Hmm Seanathon. The original script for Prometheus I read contained wall mounted larval eggs contained in a huge chamber as well as urns and much more engineer content. I don't quiet understand your comment unless we read different things.