In the commentary for Prometheus, Ridley acknowledged the size discrepancy between the jockey and the engineer. He said he felt it was more important to have an actor playing the engineer be physically on set with the other actors, rather than awkwardly green-screened in.
This is a good example of how Ridley focuses on making each individual movie the best it can be, even if it comes at the expense of canon and continuity.
It drives us fans nuts, but I'm sure a lot of creative types get it - (and us fans usually manage to fudge together an explanation anyway.)
Ridley clearly wanted that moment between David and the baby. He wanted to express the relationship by having it mimic David's pose. This scene wouldn't have played as well if it didn't have arms and just stood straight like a snarling boner.