I think the OP is confusing the runtime and image format a bit here. At runtime OverlayFS can use metadata-only copy up to describe changed files, but the container image is still defined as a sequence of layers where each layer is a tar file. There's no special handling for metadata-only changes of a file from a parent layer. As the OCI image spec puts it [1]:

> Additions and Modifications are represented the same in the changeset tar archive.

[1]: https://github.com/opencontainers/image-spec/blob/02efb9a75e...