Even though the icon appears to be a regular folder icon with some icon over it, it's still a custom icon -- the same as if the icon looked completely different from a folder entirely. Short answer is that it's not a regular Mac OS X folder icon with a littler icon hovering over it -- it's a different icon altogether make to look like a regular Mac OS X folder with a littler icon hovering over it.
To change a folder's/file's icon, do a "Get Info" from the File menu while the file/folder is highlighted, and you can copy and paste icons right into the Get Info window by clicking on the icon, then pasting your new icon.