How is this better in that way? Users and site administrators rarely have direct access to skins, extensions, and the site configuration itself. Unmaintained css, wherever it is, will 'die'. Changing the functionality of existing features will simply break stuff, as what is proposed cannot be backwards compatible. As people have pointed out already, being able to customise the overall appearance of an existing skin is expected and well-used functionality. There is no good reason to remove this.
Adding a separate content-scoped css interface message that would be called after common.css and skin.css might not be a bad idea, however, since that way users could put all the content-specific things there. Be a little neater away from the wider-scope stuff, and since it's all content anyway, definitions could be a bit shorter since the #content bit would be added automatically...