What we call a brute fact is what Aristotle would call knowledge that something is true without knowing why it is true. Ironically, while brute facts occur most often in attempts to halt cosmological arguments the conclusion of the cosmological argument is itself a case of only knowing that something is true.
Aha! So as long as we posit a BF in either case, why not take the universe as one and treat God as a superfluous addition? But this is to be tricked by the mere repeating of a word: if the universe is a BF it is because there is only one of them and so we cannot run multiple experiments on it, or because it is (probably) fallacious to extrapolate from truths about parts of the universe to truths about the whole (cf. Lee Smolin’s Time Reborn). But God is a BF because to know what God is belongs only to the blessed.
More simply, the B-facticity of the universe is given to sensation while the B-facticity of God is not. One wonders how much of the talk about “brute facts” involves a failure to recognize the false assumption that the first sort of facticity is the only kind.