What if that system of inequality is biology? Is is still absurd to treat them equal?

Sometimes, sure. For example, if there's some task to be performed, and because of their biology X is capable of performing it and Y is not, it's frequently absurd to behave as though X and Y were equally capable of performing it. Having a long "conversation" with a deaf person who is not looking at me can be absurd, for example, as can giving a pregnancy test to a man.