Hmm, after having this in the back of my mind I have the ideal solution, but it will require some work.
Store the CSS attributes in the database. Then you can manage them in one place, but still use multiple CSS files with almos t the same contents. Using the content repository you could build up the CSS file and publish it to the filesystem.
This won't work without some code, and any CMS effort we work on should include at least some support for CSS files.