I reinstalled gentoo, with the ~x86 flag today, and noticed that portage kept complaining it couldn't find pkg-config (untill it was later installed). It should be fetched as a dependancy.
Closing, portage (ebuild.sh, specifically) doesn't require pkg-config- you likely hit a borked ebuild. Possible it was an eclass attempting to access pkg-config in global scope (gtk-engines 1 or 2 do this) also.