I agree. I wouldn't rush to draw any conclusions, as this paper changes the status quo. We can not say anything about the rarity of transmission events in the past really. This work is focused particularly on heteroplasmy -- it doesn't rule out other causes.

It does not seem we understand the mitochondrial inheritance mechanism during conception.

We can set an upper bound on paternal mitochondrial inheritance: there are hundreds of thousands of mitochondria in an egg, and tens in a sperm.

If all paternal mitochondria were transferred every time (unlikely‡), then a child's mitochondria would be ~99.99% inherited through the mother.

‡ Unlikely because sperm mitochondria are located toward the flagellum in order to power locomotion, and the capsule at the head is normally the only part which fully penetrates the cell membrane.

Ref: https://www.quora.com/How-many-mitochondria-are-there-in-hum...

Does that not assume that the mitochondrial from both parents are treated equally in terms of inheritance? It seems to me that biological systems do not tend to use random chance most of the times if there is a evolutionary benefit, thus if there is such benefit I would predict that those "tens" would be treated differently from those hundreds of thousands.

I was mostly talking about the concept of mitochondrial incompatibility, which is significantly more common than what is discussed in the paper, which is paternal inheritance. I made a note of it being doubly rare (female must survive to reproduce age with a specific mitochondrial sort of defect)