If it is not immoral to love one's own children more and put them above all
Let's start with your second sentence: "Biological polygenesis and philosophy of history make it clear that colonialism and destruction of indigenous cultures is not always immoral." A few obvious points.
First, biological polygenesis (distinct origins for different races) is not widely accepted among scientists. In fact, far as I know, the evidence points in the opposite direction.
Second, even if polygenesis happens to be true, that wouldn't show that colonialism and destruction of indigenous cultures and peoples was okay. Compare: suppose that sometime in the future, humans travel outside the solar system and find intelligent creatures on other planets. Those beings certainly have different origins than we have. But from that it doesn't follow that we would be justified in colonizing them, let alone destroying their culture or killing them. After all, if intelligent aliens make it to earth, that wouldn't make it right for them to colonize us or kill us.
And finally, "philosophy of history" doesn't show what you claim without a very specific, detailed argument about particular cases. No doubt such arguments have been offered. Whether they are any good is another question.
But let's go back to the question you begin with. Let's agree that it's not immoral to love your own children more than other children. That doesn't allow you to ignore the welfare of other children. It doesn't justify you in doing things that actually harm other children. And it certainly doesn't give the law any reason to favor your children, or mine, over anyone else's.
Our emotional attachments are a complicated business. It's true: most (though not all) of my friends are white, like me. But that's a very different thing from my having some sort of general preference for the Caucasian "race" as such. If I subscribed to all sorts of peculiar beliefs about people of other races, I might end up with that attitude. But there's no reason to think the beliefs would stand up to scrutiny. In any case, it would be one thing if, as a matter of psychological fact, we tended to prefer people of our own race to people of other races. But if I think it would be wrong for me to treat my white neighbor in certain ways, then I ought to think it would be equally wrong if my neighbor wasn't white.
Maybe humans will always pay attention to skin color. What they make of it is another matter. My daughter and her friends are much more "color-blind" than people were when I was her age. This strikes me as a very good thing, which brings us to the point we'll end on. In spite of what you seem to suggest, it's hard to make the case that racial preference has done the world any good and easy to make the case that it's done a lot of harm. Extending concepts like love of one's children or love of one's friends to love of one's racial group is skating on micro-thin moral ice.