If I understand correctly, the usual process of metabolic syndrome and obesity is that the muscle cells become insulin resistant at a faster rate than fat cells. Thus insulin starts rising to compensate for the sake of muscle, but the fat cells, which are still sensitive, take this signal at face value and store more fat. It makes sense that adipose tissue insulin resistance would limit fattening.

I'm guessing that what is damaging the mitochondria is ROSs. Cell membranes are made of highly polyunsaturated fatty acids, which are particularly susceptible to such damage.

My current hypothesis is that people who have difficulty with carbohydrate metabolism are not properly coping with the normal ROS production involved in carbohydrate metabolism. So the inflammation is not being cleared, and it is damaging surrounding cells. Why muscle cells would be more susceptible, I don't know.

This could explain, in part, why switching to a ketogenic diet often and stops and reverses the process -- ketones don't generate as much oxidative radicals when used for fuel, and they are also antioxidative.