According to LKML https://groups.google.com/d/msg/linux.kernel/O7NO7Ez5Axw/_--m_euINzEJ when using both CONFIG_EFI_VARS=y and CONFIG_EFIVAR_FS=y "it should be noted that because no synchronisation is performed it is very easy to create inconsistencies". CONFIG_EFI_VARS is old and limited, but it's required for efibootmgr. According to Arch https://wiki.archlinux.org/index.php/UEFI#Inconsistency_between_efivarfs_and_sysfs-efivars they're using patched efibootmgr which works using CONFIG_EFIVAR_FS. Maybe this patch should be also added to Gentoo?
efibootmgr support efivarfs since version 0.6.1 See : https://bugs.gentoo.org/show_bug.cgi?id=510070 In the meantime I added ebuilds for efibootmgr 0.8 in my personnal overlay : https://github.com/Wyti/Wyti-Overlay fell free to use it and repport any issue you might have on the github tracker.
Should be fixed with efibootmgr 0.11.0.
