Finally to wrap this up, your quote:
Ultimately, I think the false boundaries around science and philosophy aren't helpful as we need both working together. Without science and technology, philosophy would be so out of touch with reality (as we're best able to perceive it) as to be unhelpful and without philosophy to explore the (currently) unknown boundaries of knowledge within our conscious experiences, science would lead to things like eugenics which we later regret from a moral perspective.
To address your concern, what evidence is there that philosophy and science aren't already working together? Science supplies the facts while philosophy tells us what we should value. Philosophy and science have always worked together.
My opinion is only philosophy can explain the origin of life because philosophy provides explanations. Mathematics provides models. Science provides facts. So science is our fact generator where models are proven or disproven, where an explanation from philosophy can gain or lose credibility. The many worlds interpretation of quantum physics for example is a mathematical model but not science because it's not testable. String theory is a mathematical model but not science because it also isn't testable. Darwinism as far as I know isn't science, and the theory of evolution includes some processes which are testable, but some which are not testable or falsifiable but more just attempts at explanation, like the origin of life which I think is a mistake to try to use science there.
Whether the theory of evolution is science or not, it's extremely successful as a theory, very useful, and plausible. On the morality of eugenics, I don't think eugenics is immoral. What was immoral was how they tried to implement it. What was immoral was the complete disregard for individualism, human rights, consent, in favor of forced sterilization. Negative eugenics or coercive eugenics isn't wrong because designer babies are wrong or because intelligent selection is wrong, but it is wrong because a central state authority did eugenics without consent amorally.
If there is consent then nothing is immoral about two adults choosing to mate with each other to create what they perceive to be a master race. Nor is anything wrong with parents who genetically modify their offspring to cure diseases, promote athleticism, intelligence, or beauty. In fact under utilitarianism the case for eugenics is actually much stronger in favor of it being moral if done with consent.