“Given the standard idea of our planet having formed from swirling masses of solar material, you’d expect all the heavy metals to be at the center and nowhere near the surface.”
There are several reasons they appear near the surface.
The most obvious would be that they arrived here via impact events after the Earth was long since formed up. In that case, any ages you were to deduce from heavy metals, would apply to the heavy metals themselves but not to our own planet.