It depends on the kind of theism being considered. For instance, Einstein was comfortable believing in the God of Spinoza in light of the evidence of nature, but this is a distinctly different conception of God compared to, say, the God of the Abrahamic religions.
In Christianity, for example, believers often appeal to concepts like the Fall of Man and the resulting curse on creation to explain away suffering and imperfections in the world. They also point to the influence of Satan as an antagonistic agent who willingly rebelled against God and exerts some degree of volitional influence over creation. Christians claim that, after the second coming of Christ, all of creation will be "upgraded" to a perfected state, resolving issues such as divine hiddenness and the problem of evil.
Other forms of theism likely have their own workarounds and ways of making sense of the data in different ways.
That said, under naturalism, the laws of nature are brute facts. As such, it is entirely conceivable within a naturalistic framework to imagine an alternate set of laws of nature, which are also brute facts, that would render the universe perfectly hospitable to life everywhere, contrary to what we see. On naturalism, there is no inherent expectation for the universe to be inhospitable, perfectly hospitable, or anything in between, as any scenario would equally arise from the brute facts of the laws of nature. Similarly, one could postulate different versions of theism as brute facts that also align perfectly with the observed data or under which we would expect something completely different to the data.
In the end, without an objective probability distribution over "brute facts," claims like "brute fact set X is more probable than brute fact set Y" are utterly unjustified mathematically, whether those brute facts are naturalistic or theistic or whatever you like.