I would agree that MODing is a pain with more than one style. I had four on my site, but now down to one, just because of the portal I built for my site. Was too much to make the custom changes to the overall header, plus all the new button and images to create to match the new styles.
I am trying something new, to go through some subSilver-type themes, make them more like subSilver in code, and use EasyMOD to install. Of course, going through non-compliant MODs make it much more painful, but what else do I have to do with my free time??