It's important to realize that methodological naturalism is not only an assumption within science, but also delineates the boundaries where science can be exercised (effectively anyway). Science (all science and not just evolution) seeks natural explanations for natural phenomena. Natural explanations pertains to the methodology of science, and natural phenomena pertains to the boundaries of science.
The concept of uniformitarianism (existing forces having operated uniformly from the origin of the universe to the present time) is a weaker case of scientific 'assumption', since variations in fundamental forces, energies, particles, etc. can be measured very precisely, with no indication of mutability. But beyond that, yes, it is an assumption of all science (again not just evolution), and without it arguments such as Dad's split/merge diatribe become just as valid as science. Along with 'Last Thursdayism' and the Matrix movies. Without uniformitarianism, science loses its predictive capabilities, and since science has shown itself to be highly predictive in nature, uniformitarianism appears to be a valid assumption.
Science also indirectly accepts all the assumptions (axioms) of number theory. Again, since these work in all cases without exception, they seem to be very good assumptions.