I don’t know how well that metaphor works since Illyrians are aliens. The Federation is already full of aliens with biology and abilities different than humans. So what if Illyrians have modifications that make them different than humans? Vulcans have two sets of eyelids and are adapted to live in harsh deserts humans can’t survive in. They’re also telepathic, three times stronger, and have perfect memory.
Does that mean the Federation is a segregated society between all different races? If they split cities between Illyrians and non-Illyrians, wouldn’t they also be splitting cities between Andorians, Vulcans, Tellarties, etc.?
But the Federation has no history with the Illyrians. The Illyrians weren’t forced to live in Federation society. Their ancestors weren’t enslaved by the Federation. Their planets weren’t conquered by the Federation. As far as we know, they’re not refugees who had to flee into Federation space.
It would be different if Illyrians had always been a group within the Federation. But they chose to go to the Federation with full knowledge of the Federation’s laws. They have the choice to reject Federation membership if they wanted.