Yes life is very complex. So is tomato soup. I can make tomato soup without having a clue what is going on, chemically, in my bowl of soup.
I can know how to make tomato soup without knowing what is transpiring chemically in my soup. I can know that tomato soup has been made, without knowing what chemistry took place in the pot.
In a similar way we can know that evolution has occurred and that species share common descent, without having very detailed knowledge of all the chemistry that occurred during that evolution. And we can know it so well that we can call it a fact, despite being largely ignorant of many specific physical and chemical details.
I can tell someone to use warm water and soap to wash their hands, and I can tell them that this will kill and wash off the majority of bacteria on their hands, and they can know that it really does work without knowing how, chemically, warm water and soap achieves this effect.
Washing our hands with soap and warm water is effective, and we can know it is effective so much that we can call it a fact, without having the slightest clue what the soap is doing chemically.
It is no different for historical inferences. Again we can derive knowledge about historical events to show us that they occurred, without having very detailed knowledge at the level of the physics and chemical reactions between individual atoms and molecules. It is a fact that plate tectonics has resulted in mountains. And I can know this is a fact without knowing the vast, vast majority of what there is to know about about the chemical constituents of the mountains. I can know that a meteor hit the ground without knowing anything about what chemistry happened in the meteor, or the point of impact.
Tour’s demand for chemical detail in these very large-scale evolutionary transitions he speaks about (such as the evolution from single cells to organisms with brains) to be able to say that something is a fact is misplaced and does not stand up to scrutiny. While that knowledge is obviously both desirable and fascinating (and a topic of active scientific investigation), it is strictly not required to know that evolution occurred and that it is a fact.