Effective altruism is based on the core belief that all people count equally. We unequivocally condemn Nick Bostrom’s recklessly flawed and reprehensible words. We reject this unacceptable racist language, and the callous discussion of ideas that can and have harmed Black people. It is fundamentally inconsistent with our mission of building an inclusive and welcoming community.
— The Centre for Effective Altruism
I think what Habryka is saying is that while EA does have some notion of equality, the reason it sticks so close to mainstream egalitarianism is because humans don't differ much. If there were multiple species civilizations like those in Orion's Arm for example, where multiple orders of magnitude differences in abilities are present, than a lot of stratification and non-egalitarianism will happen solely by the value of freedom/empowerment.
And this poses a real moral dilemma for EA, primarily because of impossibility results around fairness/egalitarianism.