There are a number of rebuilds that can be done as static code analysis. The advantage is, of course, breaking a lot of chicken-egg problems. The class registry is one. The oft-debated hook registry is another. Right now we are building this on-the-fly using the cache layer but this is not quite cache. This of course requires. For radical simplifying we could do the theme registry as well -- we are already passing in a single variables array and so hook_theme() is much less necessary. So based on the name of functions and the .tpl.php we can build up the theme registry. It'd be great to have CMI for storing this. We will figure it out what to use instead for now.
When you enable a module then a rebuild.php runs. If you add a new theme function / hook, you run the same.