Overlayfs, aufs, etc. are really irrelevant to containers. They are used in Docker because it's built around opaque binary disk images that do not compose, which I believe is a big flaw, but it doesn't have to be this way. For example, GNU Guix has a container implementation that does not use disk images at all but still achieves system-wide deduplication of software across all containers running on the host via simple bind mounts.