For microwave hot chocolate, why pour the hot milk into the chocolate rather than mixing the milk with chocolate then heating? I read on the back of the unsweetened Hershey's cocoa powder box that I should first heat milk in a microwave and then pour into another cup with the powder, salt and sugar. This tasted much better than when I directly mixed in the powder with milk and heated.
What exactly is causing the taste difference? i.e: are there any scientific explanations for the above?
You were using real cocoa powder, not an instant drink. You probably cooked it in the microwave, or at least part of it. When milk over the powder, it was certainly not hot enough to cook the powder. So beyond any lumps that might have come together (you don't describe if you took measures against it), there is certainly a taste difference between cooked and uncooked cocoa.