Suppose I have 2 gpg keys. The first is located into /home/ago/.gnupg and the second in /media/gnupg/ If my PORTAGE_GPG_DIR is set to /media/gnupg is expected I would use that key, but portage take the conf from /home/ago/.gnupg/gpg.conf
Portage should be using the command defined by PORTAGE_GPG_SIGNING_COMMAND. The default value from /usr/share/portage/config/make.globals is: PORTAGE_GPG_SIGNING_COMMAND="gpg --sign --digest-algo SHA256 --clearsign --yes --default-key \"\${PORTAGE_GPG_KEY}\" --homedir \"\${PORTAGE_GPG_DIR}\" \"\${FILE}\"" Maybe we need to use some different options.
repoman support has been removed per bug 835013. Please file a new bug (or, I suppose, reopen this one) if you feel this check is still applicable to pkgcheck and doesn't already exist.