Pretty much this. They're test subjects to him. Humans could be like monkeys to him. Monkeys in a part of the lab that they shouldn't be in. People keep saying that humans are supposed to be close to Jockeys in make up, but we aren't Jockeys. Why would the engineer treat them like equals? Look at how a lot of people regarded black people 60 years ago even though we're all the same species. Now imagine a creature that has a much longer life span than us, bigger, stronger, smarter and so advanced that it travels the universe and creates life as an experiment. I doubt they would view us as equals and treat us kindly.