Having multiple definitions for a single module is used to make one module be composed of many parts.  If you put that module on a page, all of the definitions will be created.  For example, you could have a module with a display definition and a search definition, which would drop both modules onto the page whenever you choose to add that module.

The different modules definitions will be pointing to different controls, so if you wanted different look/feel/functionality in different portals, it may just be easier to package the new look/feel/functionality into a completely separate module, or to encapsulate those differences into module settings.

Does that help/make sense?