No expert here, but I would guess the important bit is the "root": value, which in the example points to rootfs. rootfs, I suppose, would be the directory on the host system containing the entire root filesystem that is to be mounted at /. This could be created using overlayfs, or a COW filesystem like btrfs, which would be how you'd achieve layers.

In this way, the notion of layers is external to the container spec.

Again I'm no expert, so corrections welcome.