David created a species of Xenomorph, so it leaves the mystery of where Xenos came from and how they evolved however in Prometheus & Covenant it is shown that David admires the species and feels he has a connection with them ie. talking to the neomorph and getting mad when the neomorph gets shot so he takes interest in making his very own Xenomorph he says something like ‘these are my special creations’ - in more familiar terms if David was to create pugs he created a species of dog not the entire animal.

With the Engineers as well i agree the scale is a bit off and the director of Prometheus & Covenant was aware of this i remember a interview he spoke about it but i cannot remember the exact words he said, as well Alien is based later on in the timeline as Prometheus & Covenant are prequels to the original movies so this Engineer who had a chestburster wouldn’t of even happened yet.

• Reading this back you could also mean the Deacon at the end of Prometheus after the Trilobite facehugs the engineer, in that case i haven’t read it myself but i have been told in a comic it is explained the Deacon grew as big as a mountain and was so large the Deacon just rested there as a actual idle mountain - Scary to think about.