Krakoa really reminds me of West Africa, more specifically Liberia, established for emancipated American slaves and thus similar reasons for Krakoa, and Sierra Leone, Liberia's neighbor and splitting off from the UK again for the same reasons. The establishment of Liberia back in the 19th century was supposed to be seen as something similar to OP's thoughts -- by giving slaves a country, there would be an end to oppression, racism, and discrimination, with the West would be giving them what they wanted. The US and UK would help these countries out, like the US assisting in the building of Liberia's infrastructure in the mid 20th century, but in the 90s,
both countries suffered their own civil wars, after years of build up stemming from Western influence and the price of diamonds. The US as a whole handled that violence in...
less than great ways; not only were markets and supply side manipulated by western business interests, but Western military intervention was also weak and delayed compared to Kosovo.
But the way Krakoa and Dawn of X are written, I really feel like the Council is looking back at West African history as a warning with all the precedents but all the precautions -- the flowers are somewhat analogous to diamonds, obviously there are different factions starting to bubble that would split apart the nation (Apocalypse, Sinister, and we still have Moira to contend with), the humans are the West tepidly respecting the idea of mutant rights and autonomy but really wanting the financial power behind the nation of Krakoa, and all the violence that comes from it.
So in the real world, I really do think this can still be a metaphor for discrimination, but now we're not just talking about interpersonal, individual discrimination (like racial or sexual minorities) as usual, but the real effects of institutionalized, systemic forces of oppression on a vast, well-funded, international scale against a mutant (as-Black) nation. The summit between the human delegates and Charles, Magneto, and Apocalypse made that comparison on the nose. And the massive wave of George Floyd/Breonna Taylor protests and their aftermath also indicate that even if BLM got each and every one of their demands met, those systems of discrimination and oppression *will* reassert themselves if it doesn't mean changing the minds of policy and lawmakers -- i.e. the vast majority of major US cities that committed to either reforming or partially defunding the police still haven't instituted a single policy change since May. So the other nations of Earth agreeing to Krakoa's own demands is meaningless if Krakoa keeps getting attacked anyway for the central fact that they're still mutants.