I don't know, it seems more likely for users to add files to the music directory (including adding them to id1) than to open up a mod's pak file and delete or rename files in there.
I'm thinking of, for examples, the way map files are referred to by name in the trigger_changelevel, and the way skyboxes are referred to by name in the worldspawn.
These are both cases where users often install more and more content over time, and the extra bsp files and skyboxes clutter up the same directories without breaking the previous ones.
Imagine if installing a new quoth map with its own skybox would cause all other quoth maps to use the wrong skybox.