The 0.8.x versions of igraph contain additional bundled libraries not covered by the unbundling patch:
plfit and prpack aren't packaged in Gentoo yet, but the others are.
igraph developer here.
igraph 0.9 support using external versions of dependencies where it makes sense. See the new installation docs on how to do this: https://igraph.org/c/doc/igraph-Installation.html
For the rest (notably: bliss, cliquer, plfit, prpack), do NOT attempt to unbundle them. igraph contains modified versions, with either fixes or adaptations.