I believe that it has to do with denaturing the proteins that are found in the milk (or cream).  When boiling water is added to the crystals/milk, the protein in the milk is broken down (denatured) by the heat and produces a specific taste.  When you add boiling water to the crystals alone and dissolve them into coffee first and then add the milk, there is sufficient time for the water to cool and not denature the milk.  The other thought is related to the change in the overall nature of the dissolved coffee crystal liquid that helps to "protect" the milk from being curdled.