distutils-r1.eclass modifies the HOME variable. This is forbidden according to PMS. A possible solution would be to call _distutils-r1_create_setup_cfg from esetup.py, to ensure that ${HOME}/.pydistutils.cfg. This requires some testing to ensure we don't break stuff that relied on pydistutils.cfg persisting between function calls.
commit da4e991e2ac745a1d202b964072b69d3bf4bbd01 Author: Mike Gilbert <floppym@gentoo.org> Date: Sun May 29 08:57:59 2016 -0400 distutils-r1.eclass: Do not modify the HOME variable This was only necessary when we ran phases in parallel. Also, PMS says this variable should not be modified.