How? For starters, the characterization of the sciences you offer sounds like those of a true believer instead of a scientist or scientifically inclined theologian, say the Pope, who embraces science and evolution. But, I can offer a rational response, which you are welcome to decline and downvote in your efforts to proselytize. Given your references to your faith in Scripture, and from your bio:
The work required to bring [Spinoza's] massive accomplishments to the attention of the widest audience possible will require the participation of as many like minded [sic] souls as possible who are willing to assist. The resurgence in Spinoza research and explosion of commentary within the extant, indicate that something important is afoot.
Now, to address your question, not as a believer, but a skeptic, it follows such:
One. There is no ONE scientific method; varieties of the method create the philosophical problem of the demarcation of science. So, immediately you start with a canard. When one has a genuine desire to understand science, one appeals to contemporary philosophy of science for understanding, not a mischaracterization of science that is favorable to one's metaphysical presuppositions. Each flavor of science whether biological or physical, natural or social is effective generally, though each has limitations. One cannot pray rockets to the moon.
Two. Good scientists don't practice science faithfully, though scientism can be seen. Rather good scientists practice science skeptically, because they believe that faith is a poor pathway to objective facts. Some scientists become philosophers and are concerned with truth certainly, but post-postivistic philosophy of science concedes fallibilism which many scientists accept as a given since the program of the logical empiricists and postivists failed spectacularly. No serious philosopher of science pushes the idea that subjectivity can be removed from the method, since everything from observations to experimentation to theory selection is value-laden. Some scientists believe that it is not even possible to know "reality" and accept the inherent limitations of thought and are known as instrumentalists. In short, philosophers of science concede that scientists are inherently biased one-way or another, which should have been a surprise to no one, though it still seems to stun certain thinkers. Thus the necessity of peer-review.
Three. SOME philosophers of science believe that knowledge does not "reside" in nature, as a "soul" resides in a body. Post-Cartesian duality, it has become clear to many philosophers of the mind, including but not limited to Gilbert Ryle, Jaegwon Kim, Daniel Dennett, and others, that propositional knowledge is an organization of the brain based on experiences. Far from being a superstition, thought is generally acknowledged to be a phenomenon whose behavior and basis is rooted in the central nervous and endocrine systems, and is best embodied by the slogan, no-brains, no-minds. This, of course, is reasonable since it comports with common sense and everyday experience.
In your prior question, you ask after the nature of philosophy and talk about those who use mathematics, science, and formal logic as a tool and those who avoid it favoring "natural language". To understand the analytical philosophical tradition, the quotation from the article by Russell:
Modern analytical empiricism [...] differs from that of Locke, Berkeley, and Hume by its incorporation of mathematics and its development of a powerful logical technique. It is thus able, in regard to certain problems, to achieve definite answers, which have the quality of science rather than of philosophy. It has the advantage, in comparison with the philosophies of the system-builders, of being able to tackle its problems one at a time, instead of having to invent at one stroke a block theory of the whole universe. Its methods, in this respect, resemble those of science.
Given your question:
The Scientific method purportedly achieves the deriving of objective truth by removing the unavoidably subjective nature of human knowledge from the loop. This system claims that by following certain procedures faithfully, the knowledge resident in nature can be brought forth and 'captured' without any human intervention. How is this even remotely possible? It sounds like a form of superstition, like belief in an anthropomorphic god.
Mystical, faithful, and transcendent might be used to characterize the philosophy of Spinoza, but I welcome any contemporary philosophical references that characterize science that way because the philosophy of science has a strong factual history rooted in the rational, empirical, skeptical, and common-sensical methods.
Can one speak unambiguously of “The” Scientific Method?