pari has assembly kernels for several architectures, as well as a reference C kernel for other archs. If you just run ./Configure it chooses its ix86 kernel, but the ebuild passes --host=${CHOST} to Configure, and for the standard CHOST of i686-pc-linux-gnu that fails to choose the ix86 kernel. If the ebuild will continue to specify --host (rather than letting Configure get it from uname(1)), it should munge CHOST to just arch-os, eg i686-linux. Perhaps something like: --host=${CHOST/%-*/}-linux or just let it get it from uname(1).
Thanks for the hint. Fixed in -r1. Decided to use --host="$(echo ${CHOST} | cut -f "1 3" -d '-')"