I haven't done the research, so this is conjecture: "unnatural" is rooted in more of a moral observation or declaration, than a literal* or observable one. The concept of Sin disrupting the purity of the physical world (the whole of nature) and spiritual world leads to assessments of "unnatural behavior". The most obvious references comes from moral codes in the Bible, particularly the Old Testament. Lots of important moral observations and rulings on what should and should not be acceptable "natural" behaviors. Which informed a lot of cultures for a very long time. I won't go down that rabbithole per forum guidelines.
Now, fastforward. If I saw an object be let go of by a person, and it FELL UPWARDS at high speeds instead of down, without the ability to run tons of scientific equipment I would probably think "that was an unnatural phenomena", or 'this was not by way of natural forces', like gravity or magnetism.
When you get into advanced chemistry and other sciences, there are some compounds that, very likely, meet the requirements of "unnatural". Substances, chemicals, organisms, energy experiments, can be created in laboratories that, very likely, would never exist in nature without human invention or recombination. Call me skeptical, but I do not believe that future evolution of life on earth would explain how the bioluminous genes of deep sea jellyfish would EVER make their way into the genome of trees on any scale of time. And yet, it exists. In a laboratory.
That is unnatural, but humans invented it, and we are derived from the natural world.
So, I think the older roots in morality better explain such a... logically conflicting word.
Hmmm...I'm not entirely sure what your point is. I might have you completely wrong (and if so I apologise) but you seem to be conflating natural/unnatural human choices on the one hand with the properties of the chemical / physical world on the other.
I would suggest to you that nothing of which humans can conceive or do is unnatural. It might be immoral according to certain codes, but it is not unnatural. It couldn't exist if unnatural.
As for your example of the object falling upwards. That exact thing happens in my sci-fi novel coming out next year. There is a rational explanation for it.