Oh, yea. I didn't mean to give Linux/Unix a pass. Those systems can be equally cavalier about leaving their configuration droppings all over my filesystem, too.
If in a central place what happens if the original directory is moved - how is the metadata updated. - Unix is another file somewhere, Windows can be in the registry.
With Apple it is kept with the directory.
The issue is that a directory needs some metadata and the Unix design of everything is a file does not allow the directory to include this without adding another file somewhere.