From http://bugs.python.org/issue1294959#msg94986

“The main problem is that Python's configuration system is not
geared up to having the lib directories for platform dependent
and platform independent parts use different names.

It currently only supports using different path *prefixes* for
such setups (--prefix and --exec-prefix), e.g. /usr and /usr64
would work just fine. It doesn't follow --libdir.”

So I don’t know whether there can be a simple fix for this or if we have to wait for the new sysconfig module (see http://bitbucket.org/tarek/distutils2/src/tip/docs/design/wiki.rst)