At heart is the notion of "conventional portrayal". The scientific method, as a monolithic and generalized epistemological strategy is an oversimplification of how science is practiced, but science is a complex psychological and sociological process and there are a number of characterizations of it that are quite valid but often not recognized by Latour, Feyerabend, Kuhn, and others who are often left out of the conventional portrayal.
Basically my question: is (scientifically) acquiring knowledge fundamentally based on the binary testing of hypotheses?
The answer to that is no. The basic acquisition of knowledge is based on experience which is a complicated affair to even describe. Ryle in his The Concept of Mind talks about knowledge-how and knowledge-that. I would say that the preponderance of knowledge is fundamentally of the sort called knowledge-how. We learn how to speak, not the rules of grammar, as children. We learn how to do our jobs, indeed, with the aid of language, but usually not the myriad theories that explain our jobs. (Think of an automechanic who has never studied calculus based thermodynamics.) And where we do acquire knowledge-that, we are often unaware of the metaphysical basis of our craft.
Most practicing scientists have little to no engagement in the philosophy of science, just as most practicing mathematicians have little to no engagement in the philosophy of mathematics. And practicing scientists and others, who do engage in empirical design and implementation, sometimes try to answer questions in the yay-or-nay fashion, more often than not are looking for any form of language that will give insight and serve as an explanatory basis for the phenomena they study. Let's consider an example.
Charles Darwin and Alfred Rusel Wallace were preoccupied with the origin of species. But neither man set themselves up to say, either my theory is correct or my theory is incorrect. Consequently, the theories advanced were complex and descriptive, with Darwin publishing On the Origin of Species which ranged over quite a diverse array of contexts with all the complexity of full discourse in language. The acceptance of evolution is not based on a single A/B test, but rather consisted of a complex series of arguments each of which was based in part on descriptive science.
The theory of evolution is not preserved or rejected based on one or more binary experimental tests. Rather, it happened that a great deal of analysis and testing of all sorts ultimately supports, modifies, and extends the thesis. Thus, evolution is a strong theory because it integrates the various subdisciplines of biology, conjoins nicely with genetic theory and practice, manifests a high degree of consistent and rational claims, carries with it rhetorical force, and supports methodological naturalism, an important aspect in scientific methods.
Scientific theory is the forging of robust language that requires all manner of sophisticated activity and varies from science to science. Scientific theories are complicated epistemological processes that appeal to prior science, rhetorical strategies, to methodologies of rationalism and mathematics, that presume metaphysical theories, and that engage with a diverse set of experimental methods. Science is so varied and complex, it raises the demarcation problem, and yesterday's crackpot theory might become tomorrow's science, or today's science becomes tomorrow's pseudoscience.
As such, science does not proceed merely by a string of formulaic scientific experiments and directly arrive at truth (whatever that may be).