We've had trouble in the past with this kind of patching because Portage wasn't validating properly the manifest. Furthermore, this gets in the way because it increases the number of directories (and thus inodes) in the tree itself (and I've done enough work on the subject to know that cutting down the number of directories can be significant). Then you have bug #420785 which is hard to fix because you don't know which patches to check against. So pretty please clean up this mess.
Fixed in CVS