I recently noticed that emerging world does not upgrade packages obtained with layman. I have been syncing with layman, and in fact many of the overlay packages currently installed are no longer in the tree. I suppose I could emerge each package individually to upgrade it, but there has got to be a better way. Here's the relevant part of my current upgrade process:
layman --sync-all emerge --update --deep --with-bdeps=y --newuse --keep-going --complete-graph --verbose-conflicts @world
I would think that running emerge like that would at least raise a warning that atoms are in my world file yet not in the portage tree, but I've never seen one.