With the latest portage release, tracked by bug 683434, the default configuration no longer nests /distfiles and /packages inside the main ebuild repository (bug 378603). Once the release tracked by bug 683434 has been stabilized, it makes sense to begin warning about nested directories like these. Eventually these directories can be dropped from the excludes that were added for bug 666554: https://gitweb.gentoo.org/proj/portage.git/commit/?id=b587fc874ce95064139ba85552e146da957cce9e
The warning can suggest to migrate to the new locations approved by the council, as shown in this commit for bug 378603: https://gitweb.gentoo.org/proj/portage.git/commit/?id=ef8469befbd7b61f1bae8f21ffd95e0c0306a4f8 DISTDIR="/var/cache/distfiles" PKGDIR="/var/cache/binpkgs" For a /local subdirectory, it can take /var/db/repos/gentoo as an example, and suggest to use /var/db/repos/local instead.
Note that default RPMDIR also used to be under /usr/portage (see bug 687734), but apparently practically nobody used it, since it was never a member of the default excludes.