Did animal mitochondrial evolution have a long period of stagnation?

I encountered an interesting popular article telling about findings challenging Darwin's evolutionary theory. The original article of Stoeckle and Thaler is here.

The conclusion of the article is that almost all animals, 9 out of 10 animal species on Earth today, including humans, would have emerged about 100,000 200,000 years ago. According to Wikipedia all animals are assumed to have emerged about 650 million years ago from a common ancestor. Cambrian explosion began around 542 million years ago. According to Wikipedia Homo Sapiens would have emerged 300,000-800,000 years ago.

On basis of Darwin's theory based on survival of the fittest and adaptation to a new environment, one would expect that the species such as ants and humans with large populations distributed around the globe become genetically more diverse over time than the species living in the same environment. The study of so called neutral mutations not relevant for survival and assumed to occur with some constant rate however finds that this is not the case. The study of so called mitochondrial DNA barcodes across 100,000 species showed that the variation of neutral mutations became very small about 100,000-200,00 years ago. One could say that the evolution differentiating between them began (or effectively began) after this time. As if mitochondrial clocks for these species would have been reset to zero at that time as the article states it This is taken as a support for the conclusion that all animals emerged about the same time as humans.

The proposal of (at least ) the writer of popular article is that the life was almost wiped out by a great catastrophe and extraterrestrials could have helped to start the new beginning. This brings in mind Noah's Ark scenario. But can one argue that humans and the other animals emerged at that time: were they only survivors from a catastrophe. One can also argue that the rate of mitochondrial mutations increased dramatically for some reason at that time.

Could one think that great evolutionary leap initiating the differentiation of mitochondrial genomes at that time and that before it the differentiation was very slow for some reason? Why this change would have occurred simultaneously in almost all animals? Something should have happened to the mitochondria and what kind of external evolutionary pressure could have caused it?

1. To me the idea about ETs performing large scale genetic engineering does not sound very convincing. That only a small fraction of animals survived the catastrophe sounds more plausible idea. Was it great flood? One can argue that animals living in water would have survived in this case. Could some cosmic event such as nearby supernova have produced radiation killing most animals? But is mass extinction really necessary? Could some evolutionary pressure without extinction caused the apparent resetting of mitochondrial clock?
2. In TGD based quantum biology the great leaps could be caused by quantum criticality perhaps induced by some evolutionary pressure due to some kind of catastrophe. The value of h_eff=nh₀ (h₀ is the minimal value of Planck constant) - kind of IQ in very general sense - in some part of mitochondria could have increased and also its value would have fluctuated. Did a new longer length scale relevant to the functioning of mitochondrias emerge? Did the mitochondrial size increase? Here I meet the boundaries of my knowledge about evolutionary biology!
3. Forget for a moment the possibility of mass extinction. Could the rate of mutations, in particular the rate of neutral mutations, have increased as a response to evolutionary pressure? Just the increased ability to change helps to survive. This rate would become high at quantum criticality due to the presence of large quantum fluctuations (variations of h_eff). If the mitochondria were far from quantum quantum criticality before the catastrophe, the rate of mutations would have been very slow. Animal kingdom would have lived a period of stagnation. The emerging quantum criticality - forced by a catastrophe but not involving an extinction - could have increased the rate dramatically.