Drubin: Some drivers do not have the same excursion capacity in both directions. It is therefore possible to increase the potential for a driver bottoming out when running it in reverse polarity. Due to the initial thrust, which would normally be forward but is now backward, and the inertia involved in trying to stop the cone, overshoot into the back plate becomes more of a possibility. The end result would be damaging the voice coil former and possible dragging of the cone and the resultant poorer sonics / overheating. Couple this with the fact that some people stand on the throttle trying to break the drivers in faster and you could end up worse than if you just let them "play in" gradually.
Like anything else, a product should be "broken in" in a fashion that simulates normal use. Otherwise, the "wear pattern" will not be the same as what it undergoes in normal use. Using a special disc for this purpose is therefore preferred to using the speakers in a non-standard fashion. Sean