As of v2.0.0 and config version 3, containerd supports a more advanced merge strategy for configuration that would allow the NVIDIA runtimes to be configured in their own file.
This avoids the need to modify /etc/containerd/config.toml, making the container toolkit installation less invasive and improving compatibility with tools like kubespray for long-running, bare-metal clusters that need to be able to receive in-place updates.