A clearer way to look at the mutation rates?

I think some of my problems understanding the effects of mutation rates in our model are created by the words I've been using, words that describe an aspect of what the model does rather than what it represents.

In most of the runs I've done, the genome being followed (the focal genome) mutates at a specified rate in each cycle (usually 0.0001 or 0.00001 mutations per bp), and the DNA fragments that are recombined mutate at a 100-fold higher rate. This is designed to simulate the fragments coming from cells that shared a common ancestor with the focal genome 50 generations ago. This is a biologically reasonable setup.

In the model itself the differences are handled as different mutation-rate settings that are applied to the same mutation-generating subroutine, and that's how I've been thinking of them. But I now think that referring to both types of changes (in the genome and in the fragment) as due to different mutation rates has created problems, causing me to feel that I have to justify using two different rates, and that the model would somehow be simpler or purer if the two rates were the same.

But what if I instead referred to changes in the fragments as being due to 100 generations of divergence, rather than to a 100-fold higher mutation rate? I'm going to try this and see if my thinking and writing become clearer.