Never mind, found my answer. The layup is the same and they pulled the carbon from the same stock, but the S-Works frames are the result of a process of selecting the lightest carbon fiber from that same lot and setting it aside for just S-Works frames. So it's sort of like buying the apples from the bin of regular apples or from the bin of apples selected for their better shape, texture, and color: they come from the same farm but these are the best of what we produced.
Source: Spoke to Specialized reps over the phone this morning.