utilitarianism says that each individual should be valued independently of others, and then added together to form an aggregate value. This seems to imply that each additional copy should receive full, undiscounted value, in conflict with the intuition of identical copy immortality.

What you call the intuition of identical copy immortality is a self-interested intuition: we have a stronger interest in that someone numerically identical to us survives than in the survival of a mere perfect copy of us. But utilitarianism is not a theory of self-interest: it is a moral theory. Accordingly, I don't see any conflict here. Your preference for A over B is explained simply by the fact that you are self-interested; if you were a purely impartial utilitarian, you would be strictly indifferent between A and B.