xdbdata-0.99.1 now installs to /usr/share/X11/xkb whilst xorg-server-0.99.2 still hardcodes --with-xkb-path=/usr/$(get_libdir)/X11/xkb. This leads to broken xkb support. Romoving this line entirely from the xorg-server ebuild fixes the issue here.
Thanks, fixed.