See if this works for you:
1. Select all the bucky ball polygons and run Mesh>Commands>Disconnect with the preserve groups option disabled;
2. Instead of using the Explosion FX deformer, use a MoGraph Random Effector. In the effector’s Deformer tab, set the mode to Polygon. Then make the effector a child of the bucky ball object;
3. Place the bucky ball object as a child of the atom array.
Now you can animate the random effector to create the explosion. Not quite the same controls as Explosion FX but it might do the trick.