Microwaves cook food in two ways, one being the microwaves heating the food and the other being conduction of heat from hot bits of food to cold bits. Once the microwave is off no more heat (energy) can be added to the food, it just gets redistributed by conduction. For solid food you need to leave it to stand to get the conduction to redistribute the heat evenly through the food and eliminate hot spots. For liquids, such as milk, stirring or shaking distributes the heat evenly more quickly.
In your example Visualise, when the chocolate comes out of the microwave, some of the chocolate is very hot, well above melting temperature and some is below melting temperature. Leaving it or stirring it makes the very hot chocolate a bit colder (but still above melting temperature) and the colder chocolate a bit warmer, so that it melts as heat is transferred from the hotter chocolate to the colder chocolate.