Just like the Protomorph, the Neomorph was created by a human creation/construct (David) programmed to be relatable and think and behave much like a human.
The Deacon came about through chance and randomization but is still the product of the black goo, which by all means seem to be Engineer technology. Sure, you could argue that it's randomization per default makes it "alien" but in the end humans/humanity were involved in every step of the way of the Alien creature's creation, whether by proxy or directly.
The "mystery" of the Space Jockey is that there is no mystery - they're us, or more accurately - we're them. Sure, one could claim an existential or quasi-philosophical spin/angle on the very title (ALIEN) and premise, but in the end it's just taking several decennia of movies and franchise-building and turning it on its head on the most fundamental level possible. It's like taking the Matrix or Terminator series and claim that the AIs and robots are actually made via magic spells, conjured by wizards and warlocks from some ancient world/plane/dimension, seeking to control mankind once and for all...
Like I said in my previous post: it's a bummer (a monumental bummer)
