It would be nice if portage would compare modes (permissions) when merging config-protected files. There are cases where the file mode is significant.
For example, files in /etc/grub.d are only evaluated by grub-mkconfig if the execute bit is set.
Note that bug 396153 suggests a solution for managing local permissions for *all* files, even those not protected by CONFIG_PROTECT.
*** Bug 576594 has been marked as a duplicate of this bug. ***