Meta-configs have already been generated for the core modules, although the details of specifying hierarchical configurations is still being worked out. In essence, a module would only need to have a complete XML meta-config that describes its step.rc configuration to be completely pluggable and configurable through this application. In the distant future, this standard can be expanded to describe themes and distributions. The application could concievably generate themes using only a simple user interface for all configuration. Just to clarify once more, step.rc would be maintained in all its glory - of that much you can be sure.
Themes are a nightmare currently.
Unfortunately, themes aren't about to change. Nobody is going to go through all those themes and clean them up, and efforts to create a theme standard have all fallen flat. People want to do thing the way they want to do them, and nobody's going to change that. All themes have a common hub around which they build their entire interface - step.rc. Step.rc is the rich source of all information, and using the proper tool, it can be used to gain complete understanding of a given theme.