It appears we aren't passing --enable-libunwind or --disable-libunwind, so mesa is autodetecting its presence. I noticed this because I had a broken libunwind that mesa tried and failed to link against (I rebuilt the broken libunwind, but the automagic dep still remains).
Resolved by commit f2714d748289ee25c7dc4ae3704973b88fff36a4 Author: Matt Turner <mattst88@gentoo.org> Date: Mon May 15 10:30:20 2017 -0700 media-libs/mesa: Add optional dependency on sys-libs/libunwind Bug: https://bugs.gentoo.org/618164 and available in mesa-17.1.0.ebuild.