I don’t know what you mean when you say that traditional scientists such as the alchemists “identified” themselves with the Divine Principle rather than with the material world. I rather doubt it was very often a case, even theoretically, of Tat tvam asi, but perhaps you’re thinking of some less exalted, or more metaphorical, form of identification.
In the final analysis, the fundamental difference between the traditional and modern sciences can be reduced to the question of whether one is looking “at” or “along” the world of phenomena—this is a C. S. Lewis distinction (see his short essay “Meditation in a Toolshed” in God in the Dock) that I often come back to—and whether one privileges Aristotle’s material and efficient or his formal and final causes.
As I tell my university students, the dispute between evolutionists and “creationists”—I put this word in quotation marks to show that I’m using it in a sense broad enough to include Platonists and Plotinists, as well as Semitic cosmogonists—is not a dispute over how to interpret a common set of perceptions; it’s a dispute over how to perceive, and thus over what is perceived. Perhaps you will recall in this connection Owen Barfield’s distinction in Saving the Appearances between “alpha thinking” and “figuration”. You might also want to take a look at my recent lecture “Requiring Religion” for a somewhat fuller sense of the epistemological divide that’s at stake here.