That's correct, layers are not part of the spec. It's the caller's responsibility to setup the container bundle (manifest + one or more rootfs directories) so that runC can load it. How that is done is not the concern of runC.

This is by design: it turns out layers, as implemented by Docker, are not the only way to download or assemble a container. The appc specification uses a different, incompatible layer system. Many people like to "docker import" tarballs which bypasses layers entirely. The next version of Docker is gravitating towards pure content-addressable storage and transfer (a-la git), possibly eschewing layers entirely.

runC is not concerned by how you got a particular runnable object. It's only concerned with its final, runnable form. The result is a nicely layered design where different tools can worry about different levels of abstraction.