Lyse a cell gently with mild detergents and glycolysis and many other processes will still run. Mitochondrial respiration will not – more than anything else, mitochondria depend on intricate higher order structures (even to the level of what side of which membrane-bound enzymes face the inside (the matrix) and what side faces out) that break down and need to be repaired, ideally remade following autophagy. The sacrifice of even good mitochondria by this process is worth destroying and rebuilding good mitochondria, provided proper levels of all of the building blocks are supplied.
What naturally stimulates autophagy? Glucagon. What stimulates glucagon? Fasting.
What is a deficiency of fasting? One of at least six deficiencies that contributes to the development of degenerative diseases.
An interesting experiment to try: how gently does one have to lyse a cell or specifically a mitochondrion to keep mitochondrial respiration intact? In other words, just how sensitive are these structures to perturbations of any kind?