I really like your response, but it also can help explain why I really dislike this essay.
I fully understand and appreciate that there are lots of things about quantum physics, and heck, the universe at large, that are unsolved and that we don't understand. I would actually expect that in order for us to understand consciousness better that we'll need to fill some of the gaps of the quantum world.
The reason why I didn't like the article is that I felt like it's misrepresenting the problem, as the comment I linked described. I'll try to explain with an analogy: In the late 1800s before the discovery of quantum physics, many physicists felt that the physics of the universe was solved and fully understood - the universe was basically just like a set of billiard balls set in motion a long time ago, and the future position of all those balls could be known if their states were known in the past. In that "pre-quantum" world, people still understood that emergent behavior could arise from complexity (even just classical complexity). This article just felt really hand-wavy to me by arguing "complexity is enough". For example, if a similar article were written in 1899, but then later we discovered quantum physics and eventually had a good understanding of how consciousness can arise from quantum interactions, I suppose the author could state "See, I was right - just more complexity!" But it would totally miss the point that "the missing piece" was actually the discovery of quantum physics in the first place, not just more classical complexity.
So I felt this article was strawmanning the problem to begin with. I don't have to believe in "magic" or "souls" or religion to believe that the tools we have to describe complex emergent phenomena are not sufficient to describe the subjective experience of consciousness, but Rovelli seems to be saying that "more complexity" is just the answer to everything.
I'd say don't be thrown off by the colorful language like "souls." All of science has this language problem and philosophers of science are asked to address the meaning of these kind of words all the time.
Having read a lot of Carlo's work along with Hans Reichenbach's who is coming from the same hardline empirical stance, I think what he's trying to say here is that consciousness or a soul (I prefer the term "volition") arises from natural and physical elements that we can observe. In other words, nothing about consciousness, life, etc comes from beyond the empirical. We are already looking at it.
Does that make sense? He really objects to inserting a god or other axiomatic beliefs and the "soul as entity" must go in that box.