The ebuilds installs a directory .gconfd in the homedir of the root account.
Umm, sadly the changelog doesn't state the reason for the explicit dodir:
gconf-1.2.0-r3 (06 Jul 2002)
06 Jul 2002; Spider <email@example.com> gconf-1.2.0-r3.ebuild :
added a hack to parse all installed gconf files and fix permissions.
killing gconfd almost everywhere installing
a quick addendum to create /root/.gconfd as well
Hm, 2002 predates EAPI and per-package HOME, so I doubt that this is still needed. But it is amazing how much permanence some things have. :)
Also (according to the FHS) /root is only the default location for root's home and subject to local preference. So it is purely the system administrator's territory and packages shouldn't install anything there.
Yeah, but the problem is that gconf has a long story of causing sandbox violations on reverse deps when he cannot play "freely" under /root/.gconfd
The issue is probably now not so important as in the past because gconf is deprecated for ages and less used but I am unsure if stopping installing that dir will start to cause other (likely old) packages to start failing :|