Let's start with the real reason I looked at fontconfig: it needs an elibtoolize call to work fine on Gentoo/FreeBSD (where fine is intended as "it does name the libraries the linux way instead of the fbsd's one that breaks every and all the binaries linking to it"). A part that, I've seen it hardcoding /usr/X11R6 paths, shouldn't that be dropped as all Xorg in tree is in /usr since a long time? Still having /usr/X11R6 paths can create problems whenever /usr/X11R6 is dropped.
I don't think we will drop the link anytime soon X11R6->lib ? Anyway, it's a relic of ancient times where we had to make sure we compiled against the freetype libs we wanted iirc, so it can be dropped if you make your changes.
done in 2.3.2-r1