It’s important to remember that Earth has an outsize influence on the Federation. The capital is, and always has been, there, and will continue to be until such time as it secedes entirely from the Federation after the Burn. The Academy is there. Starfleet is headquartered there, and grew out of United Earth’s space service. Most of Starfleet is human, most Federation colonies are human. Azetbur was mistaken to call itself a “Homo sapiens-only club” but the fact is that from the beginning, as the only planet with friendly relations with Vulcan, Andoria, and Tellar Prime, as the very reason the Federation exists… Earth found itself with a power dynamic that highly favored it.
As such, I don’t think it’s too surprising that a specifically Earthican problem could weigh heavily on the Federation, even as it grew larger and more cosmopolitan.
Another key takeaway from this that I hadn’t considered before:
Augments aren’t just banned from Starfleet. They can’t become doctors either. Speaking as a Jew my people know firsthand that one of the best ways to create an underclass is to restrict the occupations available to them. Are augments systematically kept out of skilled professions, denied the chance to better themselves and their fellow sapients? Very disturbing possiblity.