I see the problem...You have a very antiquated understanding of epigenetics. Epigenetics is the study of ALL heritable changes in gene function that occur “without a change in the sequence of nuclear DNA.” But even that definition isn’t expansive enough, because now we are finding the epigenetics factors can “allow previously unseen genetic variation to be expressed.” Which, I dare say, goes right to the heart of the matter being discussed. Namely, the ability of an organism to adapt to changing environments was frontloaded by God at the time life was first created.
In the xylenase example of directed evolution a three amino acid substitution led to an enzyme that worked better at high temperature. This was accomplished by changing the nuclear DNA, thus epigenetic factors are not involved.