When mods are installed and later uninstalled, Wrye Bash Installer can manage mod files and anneal files if necessary.
On the other hand, original game files cannot get annealed in the same way.
For the sake of consistency, whenever an orphan file is to be overwritten, a cache of that file should be created and take the lowest priority - or top of the list, following Wrye's analogy.
The only catch is that this low priority cache (or virtual mod package - whatever you want to call it) should be used for internal consistency check of the game install directory. This would prevent users from having to track files that will become lost because they are original.
Example:
If I install a 7zip package or mod, overwriting original music, video or shaders from a vanilla Oblivion install, there is no way to uninstall the mod without compromising the integrity of the installation directory.
You may say, with such small number of files, it would be easy to write a text file and backup by hand. But it is clumsy and prone to human error. Besides, other games may have other number of files.
I forgot to mention that, obviously, each cache is created for the respective file that is not provided by any mod (hence, orphan) and, of course, discarded once the mod replacing it is uninstalled. Just like anneal would work with any file provided by a mod.