We could quibble about the God of the Founders, but they believed in a creator. They did not put into our founding documents that we could mate with whom we choose. Let's not read too much into them. They followed the Darwin racism that you complained about.
Now about Nazis. It's the very same with all who believe in eugenics. Who chooses and how do they know fitness? The Nazis called the Jews inferior but they were really scapegoats and blamed for all the German problems that were caused by Germans.
Stephen Hawkings would lose to eugenics bean counters.
What worries me is selection via bank accounts or size of armies.
Natural rights is unscientific to say the least
Why is it unscientific? You know of any scientist who does not believe in natural rights? What the hell are unnatural rights anyway?
Jefferson actually wanted to include freeing the slaves in the Declaration of independence, but thought better of it so that all the states would sign on to the Constitution. Jefferson failed to do that and also failed to free his slaves, even though he freed the slave he slept with from what I hear. He doesn't sound too racist if he was willing to breed with them, now does he?
The Germans simply fed off the rampant anti-Semitism that was rampant in Europe for centuries. What fed this hate was the fact that Jews seem to be socioeconomically upwardly mobile. The Nazis just took their gold and sent them off to die.
What do both examples have in common? it is men seeking power over their fellow human beings and abusing them in the process. The love of money is truly the root of all evil, another Biblical truth. Slaves were nothing but an economic tool as was rounding up the Jews for gold. Interestingly, to abuse both Jew and slave they first had to dehumanize them in some way. The Jews were compared with vermin and the slave a glorified ape. Dehumanization is the first step towards genocide, much like the unborn infant being labeled a "fetus".
So trying to figure out what makes us human and why that is important seems to be a matter of life and death, don't you think?
So what does science have to say about making humans separate from the animal kingdom?