Yes, as soon as one begins to argue that God allows mutations to happen or not happen, the problem of evil is staring you in the face. It can’t be avoided. Dance around it all you’d like, but it remains there front and center. It has nothing to do with atheism. All all-powerful, all-knowing gods have the Theodicy problem. It is not about YEC, anytime you add God to a natural process, the problem of evil arises automatically. You try to tip toe around it but it is not going to go away.