To simplify:
He complained that "they look feral, savage, uncivilized". I infer this to mean that he feels they should be civilised, but their appearance is a contradiction to this. He doesn't like this.
You made a valid point that looks are subjective anyway, but you spent a lot of time dwelling on your point that civilization is literally cultural, which misses the point. He said they look uncivilized.
The following statement, while subjective, should not be controversial. "they look feral, savage, uncivilized [...] and faces so alien and beast like"
I agree that it's a contradiction for a civilized race to look so wild, but I think that contradiction can be justified by context.