After an emerge -C bincimap, the /etc/bincimap directory remains. This should be cleaned as the application no longer assits on the system. Also, not sure what determines what goes into /etc/config-archive, but /etc/config-archive/bincimap/ still remains. Also, the default log directory remains, /var/log/bincimap. If for some reason someone wants to keep the files in these directories after an unmerge, then they should cp/mv them somewhere else. Otherwise, we're leaving kruft around for users who don't need these files after an unmerge.
Also /var/log/bincimap-ssl is left.
No modified files under CONFIG_PROTECT will be unmerged. Non-empty log dirs won't be unmerged either. That's by portage design and not a bug.