I agree that as we study deeper and deeper into the molecular and quantum realms, no evidence of the supernatural appears.
All evidence of the supernatural resides within our minds, within our imaginations and ideas.
But scientific "truths" derived from the scientific method are ultimately also all human ideas within our minds.
That said, I reject the proposition that there are beings in a supernatural realm creating this universe and interacting with its conscious creatures. I have tried to find a reason to believe this proposition, but can't find one.
The reasons why Scientific Method is being use, as way to formulate explanations (eg model, hypothesis, theory), way to test and analyze those explanations through observations (eg evidence, experiments), is to determine what is true and what isn’t true, through evidence, and not rely on personal preconceptions such as religious belief and what we personal likes or dislikes, because these lead to bias.
The Scientific Method that you are dismissing as another “human ideas”, is simply procedures and steps required to mitigate as much as possible these biases.
So instead of only accepting what we believe in or what we like, personally, we rely on evidence and data gathering and observations, data that will make our decision for scientists, to reach conclusion if a model is successful and scientific or failure and unscientific.
And when I mean observation I don’t necessarily mean what we can see with our own eyes, because these days, we use technological devices and computers, to do a lot of the observing, measuring, calculating and testing evidence, and turn these observations into data that we can analyze.
Yes, Scientific Method is a human concept, but like I said, it is concept that help us to do science and not based everything on what we like to believe.
That’s the difference between science and religion.
In science, we don’t get to choose what is factual or not factual. Natural Science or Physical Science isn’t about only choosing what we like personally.
In religion, people follow what they would like to believe, and often, these involved in believing in the supernatural, eg spirits, gods, miracles, resurrection, reincarnation, etc. They believing in people who don’t have the benefits of science, writing old holy books that often filled with symbols, with myths and fables that defied the law of nature.
We know from experiences that birds and bats have wings, not all of them are capable of flight. And we have able to designed and manufactured wings for planes and gliders that are capable of keeping us in the air (as well as engines that can propel us).
But something like the Bible, tell us of angels that look like humans, can also have wings like birds, as well as angel with one head, but multiple faces, 4 faces in Ezekiel 1. Are such beings even be possible?
So do we choose accept reality in the natural/physical world, or do we choose the supernatural ones, where something that are made up, like the 4-winged and 4-faced angels?
Which reality actually exist?
There are reasons for using Scientific Method in Natural Science and in Physical Science.
Ps There is also Social Science that have more to do with studies of human behaviors/cultures (eg psychology, anthropology) and human actions (eg political science, economics, laws, archaeology, etc), where Scientific Method are not useful or not even used.