http://www.gentoo.org/doc/en/guide-localization.xml#doc_chap8: "The first thing you should do is change the fixed and variable definitions in /usr/X11R6/lib/X11/fonts/misc/fonts.alias to end in iso8859-15 instead of iso8859-1." In xorg-x11-7.*, I guess the new path is /usr/share/fonts/misc/fonts.alias. Adding CONFIG_PROTECT="/usr/share/fonts/misc" to /etc/make.conf, might be wise to avoid overwriting when upgrading...
"...or at a global level for any application with a resource file in /usr/X11R6/lib/X11/app-defaults/ --> /usr/share/X11/app-defaults/
Thanks for reporting, fixed in CVS.