Of course if one designs a sufficiently rich digital environment, with a designed in notion of "fitness" one can use stochastic processes to evolve more fit digital configurations from less fit ones. The process can surely be modeled by a classical dynamical system in which 'more fit' is embodied as minimizing free energy, in which case this is no more surprising that that random perterbations will cause a book standing on end in the middle of a table to fall over. (Of course, the book was purposefully placed there to demonstrate the effect. . .)
If evolutionary biology really embraces these computer models and manages to shape itself into a more predictive theory as a result, the result will be a stronger scientific theory, but one far less apt as a iron with which atheistic polemeicists can brand theists as obscurantist, retrograde and anti-scientific. After all the computer runs take place inside one of the most magnificent artifacts of human craft: a computer!