> the magic in existence itself
this refers to the mystery of why anything exists at all, and why it exists in the way it does. Not the same as some special property that only exists in certain phenomena.
> There is magic even in things we understand
This again refers to the "why it exists in the way that it does" again, as fundamental forces just "are" rather than having a causal explanation. Again, not the same thing.
> Things can be understood and still magic
That's the opposite of what you were saying before, which is that there is some special element within us that can't be replicated in a machine. That would require us not understanding something, or at the very least recognizing and understanding some property that we have identified that can't be replicated in machines, which we haven't.
What is your definition of "magic"?
My definition of magic is: mysteriously enchanting; magical: magic beauty. That's from dictionary.com btw.
Something can be explainable through words or scientific study and still be mysterious, enchanting and having magic beauty.
But topics have scope. I still find value in science. I recognize that science is just the map and not the territory, and is not a final answer about any truth. Within the confines of science itself though, there are an internal set of rules that keep it consistent. Intermingling two systems only confuses the issue. I don't use dzogchen nondual meditation to analyze chemical reactions, and I don't use science to analyze the qualia of my personal experience.
That being said, there is room for going up a level and seeing where the two systems might synergize or interact, but it requires a lot of thought and effort. It's not just something you come up with off the cuff. Magic in the Harry Potter sense may exist but until there is some mechanism for measuring it and understanding it, there's no room for it within scientific methods.
It's a metaphysical issue to intertwine the two ideas, not a physical one.
There is magic even in things we understand. Gravity, magnetic forces, the ability to feel emotions it goes on forever basically.
What I've actually come to realize is the phrase, "nothing is magic" is actually nonsensical because it's a paradox.