(With reference to this post there.)

Well, that's the trick, isn't it? One of the central pillars of racial pseudoscience is the assertion that there are multiple, materially distinct "species" of humans (or, more broadly, of people). Most refutations of race science don't go any further than pointing out that this is false, because they don't need to go any further – losing that pillar kicks the legs out from under the whole affair. However, if you're designing a fantasy or science fiction setting with alien or non-human sapients that aren't just humans with funny foreheads, you're necessarily describing a world where the assertion that there are multiple, materially distinct species of people is, in fact, true.

Now, this doesn't necessarily mean that you're inherently Doing Race Science, but you do have to face the fact that you're imagining a world where one of race science's central pillars is true. Some people adopt the zero tolerance stance that positing the truth of any part of race science is just as bad as positing the truth of all of it, which is where we end up with the argument that speculative fiction has a moral obligation to depict humanity as alone in the universe. Certainly, this is a hard-line position, but it doesn't come out of nowhere.

Ultimately, there's no magic bullet solution. You just have to think carefully about what you're doing, be conversant in the history of race science in speculative fiction in order to identify the less obvious pitfalls, and be prepared to accept that some people are never going to be satisfied with any solution other than the humans-are-alone-in-the-universe approach.