Hey Kevin,
The modification plugin is not an official Beans plugin and so I can really speak about its stability, Chris at ThemeButler is the guy to answer that.
I personally believe that you don't need to use a modification plugin. Since child themes don't have updates, you can do all you modifications straight in the Totem child theme and they won't ever be overwritten. I see child theme as a starting point that you can start from, like if someone already did some of the work for you to take over and add/modify it according to your project.
Have fun,
Thanks for input! Yeah, I don't really see the benefit in using a plugin for modifications. I thought maybe there was something very specific to the theme which warrented it.