The current grub2 ebuild calls grub2-mkconfig unconditionally from pkg_postinst. If the user has written their grub configuration by hand, this will overwrite their hard work. There is currently no way to disable this. Two possible solutions: 1. Call grub2-mkconfig conditionally based on a use flag. 2. Remove the grub2-mkconfig call and replace it with an ewarn message.
Good point, i will create pkg_config phase where you would be able to configure which directory it uses with some sane default :)
Actually i did fix this already few days ago but forgot to close this bug. Lemme know if it works for you.