A subtle and yet noticeable element in SMTIV&A was the contrast between the people of Mikado that lived in direct sunlight vs the "dwellers" of Tokyo that endured cold and had palid skin tones in the absence of it.
NPCs in Tokyo even remark on Flynn having a distinct smell.
At the same time, we can take that the ones that would still have dark skin regardless of where they live would be ethnicities that stays the farthest from the idea of "plain" Yamato or Caucasian, which... we aren't shown examples of in Mikado. Hmm.
The link between demonization and oppressed minorities was more explicitly conveyed in SMT1-2:
Eugeeeeeeenics.
Now, obviously we're just talking about what ifs and beta concepts but it's food for thought that Hallelujah would be the representative side of this regardless of the angle they'd go with.