Now, it’s quite true that a scientist–insofar as he is a scientist–need not be a metaphysician nor need he explicitly hold any metaphysical principles in order to conduct scientific inqquiries. But by that very same token, there is nothing necessarily atheist about the scientific methodology insofar as it is scientific (as the history of science amply demonstrates). It may be fair to call the scientific method “agnostic”, but even so it is not methodologically or consciously agnostic any more than it is methodologically atheist. Which is to say, a scientist can engage in valid science as a theist, an atheist, or an agnostic simply because such considerations don’t affect his methodology in practice–although the scientific methodology very arguably arose from theistic principles (cf. the work of Stanley Jaki).
What Ratzinger does, and the lawyer is quite explicit about this, is to accept this supposedly methodological atheism of modern science (or, more properly, its “agnosticism”) as controlling for philosophy. IOW, he accepts that "science" in the modern sense of the word is the only truly valid form of human knowledge, and he insists that the man of faith must bow to the scientific method as exclusively valid in all areas of human inquiry. Therefore, in Ratzinger’s view, belief that there is a cause for the existence of all that exists, which we call God, is and can only be an hypothesis. It cannot be a certainty because it is not subject to experimental verification, which Ratzinger implicitly accepts as the only valid form of “modern” knowledge. In this Ratzinger is both very modern and very Modernist, exactly as Livi says. (Parenthetically, it's worth noting that these views are at the bottom of Ratzinger's extreme--and frequently expressed--skepticism regarding the validity of historical critical study of both Scripture as well as history more generally, and it amply explains his preference for subjective, allegorical approaches to Scripture.)
Without getting too far into the weeds, I’ll simply point out the misguided notions in the concluding paragraph by the lawyer. Bear in mind, however, that this is an accurate representation of Ratzinger’s own misguided ideas–which are both modern and Modernist and are deeply destructive of Christian faith:
“Between the ontological truth of the creative Reason and the transcendental presuppositions of science there is no logically necessary relationship. As stated above, scientific laws prescind from the question of the existence of God and the origin of reality. For this logical reason Ratzinger maintains that God’s remains “the best hypothesis, although it is a hypothesis” (J. Ratzinger, “Benedict’s Europe in the crisis of cultures”, Siena 2005, 123).”Now, it's not exactly true to say that “scientific laws prescind from the question of the existence of God and the origin of reality.” It might be acceptable to state that “scientific method prescinds from the question of the existence of God and the origin of reality.” Be that as it may, it is not logical to conclude from this that the existence of God is purely hypothetical. In point of fact, that statement–that the existence of God is and can only be an hypothesis–is itself a non-scientific assertion that is not susceptible of experimental verification. That is, while purporting to represent scientific method it is actually an unscientific statement by the standards that the lawyer espouses.
For anyone who wishes to really get into this topic, I recommend two classic works by Etienne Gilson: The Unity of Philosophical Experience and Thomist Realism and the Critique of Knowledge. “Critique of Knowledge” simply refers to Kantian Agnosticism. Gilson systematically dismantles the claims of Kantian thought to be either scientific or philosophical.
It may be worth noting, in light of the fact that Livi approves a form of what he calls "common sense," that in Thomist Realism Gilson devotes a chapter to rejecting certains forms of "common sense" as espoused by Thomas Reid in the 18th century as well as by some 19th and early 20th century "scholastic" thinkers. Gilson's critique is based on what he sees as the failure of these thinkers to properly distinguish between the Aristotelian (and Thomist) idea of a "principle" as opposed to a "presupposition" or hypothesis. I believe a distinction can be drawn between those thinkers and Livi and that Livi's views are probably very close to what Gilson might refer to as a principled "immediate" realism. For what it's worth, Livi's view is cited by the lawyer as follows:
Livi takes the path of a metaphysics of "common sense", defined by him as "the organic whole of those certainties about the existence of the beings of immediate experience that are always and necessarily the basis of every other certainty, that is, of every other claim of truth in judgments, both of existence and of attribution." (A. Livi, Philosophy of common sense, Logic of science and of faith, Rome 2010, page 7).