kde-apps/marble-16.08.3-r1: installs a file /usr/etc/xdg/marble.knsrc, which obviously should go to /etc/xdg.
Well spotted, same for 16.12.2.
Note that to fix it as for now you may just explicitly pass one of -DCMAKE_INSTALL_SYSCONFDIR="/etc", -DKDE_INSTALL_SYSCONFDIR="/etc" or -DKDE_INSTALL_CONFDIR="/etc/xdg" to cmake...
Thanks, fixed in git. https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f7ebc8dc9c3c2a37bf421767e673c85b0c152273 https://gitweb.gentoo.org/proj/kde.git/commit/?id=b23b1b0144355735e85e7466fca69cf41be5353e