"Scientific racism" has the same progressive origins as the other things you listed. Only a materialistic society could give birth to a scientifically racist state, a state that treats the people as a herd to be bred, homogenized and improved for material purposes. And any racism that exists in such a society can only be scientific, as any sense of community or nationhood becomes impossible in such an environment of atomization.

So the second case would be preferrable, keeping in mind that "multirracial" can only be a transitory state as given enough time all populations will inevitably homogenize. So the traditional multirracial state would eventually cease to be multirracial, and become itself an ethnostate, though a non-white one.