profiles/default/linux/powerpc/ppc64/10.0/64bit-userland inherits features/64bit-native, which sets LIBDIR_ppc64=lib64. sys-devel/crossdev-20120721 creates a make.conf, which has LIBDIR_ppc64=lib. This somehow confuses sys-apps/baselayout-2.1-r1's multilib_layout(), which now tries to create lib->lib symlinks (from lib to $LIBDIR), which is obviously wrong. I edited make.conf to set LIBDIR_ppc64=lib64, and this made the problem vanish.
that's dead code that should have been culled a while ago http://git.overlays.gentoo.org/gitweb/?p=proj/crossdev.git;a=commitdiff;h=ccd3d3050e64d0377a01843f94ef67da2ea6b665