The Debian package management system has the ability to keep a track of packages that where removed, but not with the config (i.e they were not purged). You can remove the configs by 'aptitude purge ~c'. Portage should have the same equivalent feature. Reproducible: Always Steps to Reproduce:
Also does portage have a purge option at all?.. I mean temporarily removing /etc from CONFIG_PROTECT?
In the calling environment can export CONFIG_PROTECT="-*" or CONFIG_PROTECT="-/etc" or whatnot.
That appears inconvenient, I think a purge option should be there.