Following FHS 2.2 there should be a symlink /usr/lib/X11 -> /usr/X11R6/lib/X11 See: http://www.pathname.com/fhs/2.2/fhs-4.4.html (I don't know whether this falls in the responsibility of a gentoo build though :-)
Matt, you're our resident LFS/LFH/FSH expert
Fixed in xfree-4.2.0-r9 (just remerge xfree-4.2.0-r9 to see the change take affect). Thanks for the report!