does it even make sense to depict the existence of an axis of oppression constructed on skin color and separate from nationality outside of our universe where it is a continuation of the construction of race science? does doing so actually naturalize the existence of race as a real category?
I think some of this depends on how you depict that. Like bringing an authorially critical eye to that perspective rather than, for instance, just flatly depicting it as something that is inherently or inevitably "true".
A good book to read on the false scientific basis for racialisation would be Angela Saini's "Superior: The Return of Race Science". (https://en.wikipedia.org/wiki/Superior%3A_The_Return_of_Race_Science) The book explores the history of scientific racism, and shows how racial hierarchies were a social creation by the powerful, to keep themselves in power.
If you are writing a dystopian universe, then one of the ways that can be dystopian is to parallel some of the destructive social norms from our world. But just as you would be critical of those norms for this world, you can also be critical of them in whatever world you're building.
I would say one thing to avoid would be shoehorning racialisation/racism into the world in a clumsy way. I really felt that when I was watching the Netflix adaptation of Shadow and Bone. For me that was racialising the (previously unracialised) material in a way that showed all the horrors of racism - which was pretty triggering to watch as an Asian person - without also being explicitly critical of that racism.
And also without showing anything positive of the culture that was being subject to racialisation. You only got to see the character being bullied, listening to slurs, etc. You never got to see anything positive from that culture (not even delicious food from that culture!), so there was never anything positive about belonging to that culture on display. And then the racialised main character literally had to hug it out with one of the most racist bullies in the end, without that bully ever repenting of their own racism. Not great.
On the other hand, if you're writing a universe where people are racialised, another thing to avoid would be having characters who feel as if they're there just via colourblind casting, but don't have convincing cultural roots. I'm talking about something like the Netflix adaptation of Bridgerton, where the South Asian characters in the second season weren't speaking or acting authentically in relation to their stated cultural background.
If you're inventing racialisation in your universe, then you can also invent culture, and you can root your racialised characters in their own cultures in a way that "colourblind casting" sometimes fails to achieve. You can also show positive aspects of those cultures. The entire culture doesn't have to be positive, or free from critique, because no culture is entirely perfect. But if you're talking about identity, then certainly one of my own experiences is feeling positively connected to aspects of my own culture, even if I'm racially minoritised for belonging to that group. That is to say: it doesn't have to be just about racism or hatred directed at people from a minoritised group. It can also be about what it feels like to draw some positives from your (minoritised) background.
By the way, you might enjoy reading Yoon Ha Lee's Machineries of Empire space opera trilogy. If you like Ancillary Justice I think you will probably really enjoy these books. They aren't so much about race, but they are certainly about culture.
Lee is a Korean American and a trans man. Race isn't necessarily a huge thing in the Machineries of Empire series, in that characters aren't particularly racialised or subject to racism. There's plenty of dystopia though - entire cultures are subject to genocide. The underlying world building is about how beliefs in different calendrical systems mathematically enable certain weapons and battle formations to function.
And then there are thematic tensions in the book that I relate to, in terms of what I see as tensions between Eastern and Western stances on individualism vs communalism, between the individual and the communal self. This is also played out in a militaristic culture in which obedience to a hierarchy is built into the characters' psyches.
There isn't gender-based discrimination either, but it's also one of those times where I can read a book where some characters aren't always comfortable with their own gender, or have thoughts about their gender. Rather than just seeing gender as an inherent, unquestionable thing.
Anyway, this is a very long comment from me, but good luck with it all.