Algorithm 4 on page 49 of the pms  specifies that the variable CONF_LIBDIR_OVERRIDE unconditionally overrides the directory used by the doins* functions. portage-22.214.171.124 seems to ignore the variable, as evidenced by the fact that no source file in portage refers to the variable, and that it mis-installs the libraries from the recently updated nvidia-cuda-toolkit-2.1 ebuild into /opt/cuda/lib64 instead of /opt/cuda/lib due to the fix in bug 265722. A simple grep of the portage tree reveals the only other place the variable is referenced is from the multilib eclass, the nvidia-cuda-toolkit ebuild is likely the only main tree ebuild affected by the mismatch between portage and the pms.
 numbers accurate as of git checkout 5d64265fe623adf6346ea2793e55ec0e57869dbf
to be precise, this is about algorithm 10
which is used for dolib, dolib.so, dolib.a and einstall, afais