When people say that Newton studied alchemy, what they actually mean was that he studied chemistry. He was studying what happens when you do different things to different elements. Sure he used the language of the time, but he was fundamentally doing chemistry. And the dream of the alchemists -- to turn base materials into gold -- was ultimately more or less realized when Henri Moissan created the first artificial diamond. Alchemy has a bad rep, mostly because it was shrouded in mystery and obfuscation, but at its core it was science, the pursuit of knowledge through experimentation.
The difference between alchemy and modern chemistry is alchemy is based on a mystic, supernatural view of reality, whereas chemistry assumes reality is basically natural. That makes a huge difference, and chemistry would never have gotten very far if it had stuck with the old metaphysics.
Well it wasn't really "supernatural" at the time. It was literally a theory about the natural world. It just wasn't correct, and have since been replaced with different theories and models.
I think of alchemy as early contact between mysticism and objectivity. People thought mysticism was a valid way to get info about the world. The failure of alchemy proved them wrong and may have partly led to a more skeptical "hypothesize and test" approach from the original "try to confirm religion" approach.
No, it was supernatural because it was about allegedly existing non-material entities and forces that cannot be observed through the senses, and that have will and the ability to influence the material world. Think spirits or gods. In Christianity from the beginning this was described in terms of reason versus faith.
Human beings have two basic ways of thinking about reality, the natural and the supernatural, and until modern science came along they habitually mixed the two together. So for instance if I asked someone why a tree was black, they would answer "it was hit by lightening" which is a natural explanation, and then "and the lightening was thrown by the God Thor" which is a supernatural explanation.
The great innovation of modern science (inspired by the Greeks) was to decide to stick entirely with natural ideas. It took centuries to make this change, and many battles, and it made possible modern technology.
Let me add that the way I am using the term "natural" and "supernatural" is not my invention, it is the standard way philosophers and scientists have spoken about these matters for many centuries.
