Sometimes I view the theory of evolution, much like the birth of a baby. A man and a woman of course have sex and there is sperm and an egg and eventually a developing embryo.
Theories in science can explain how a baby is born, and atheists could say "well I don't see God in that, it's just a sperm and an egg". But from a theistic perspective, call it "theistic birth", God creates life. God brings life into existence. This being something that no human can truly do. Only God can truly create life.
And belief in atheistic or theistic birth, is a philosophical position that is independent of the physical nature of birth. Whether God is absent from birth, or whether God is actively present in creating life, is an independent discussion from the physical nature of birth itself.
The same goes with the theory of evolution, There can be some people who say that God is not seen in the theory, and some people who say that they can see God in the theory, but ultimately it is a separate discussion from the physical theory of evolution itself.
And we can see God in the act of creating life through birth, even without needing to see God defy physics to do it.
And even when we call something "random", like, I flipped a coin and the result of the flip was "random", even if atheists may say it is random, we ultimately know that God is in control and nothing happens beyond God's will. Even a coin toss is not truly random because God is always in control.
So when atheists say "well those mutations are random", they may appear random, just as a tossed coin seems random if it lands on heads or tails, but we know that God is truly in control of all creation, with or without observed physics defying miracles. Nothing is ever truly random in this world, we just call flipping a coin random by habit as something that we simply cannot predict.
Mutations being unpredictable to us, results in us calling them random, even if we know that God is ultimately in control.