I think the point of checkbox is fine as long as they default to prefers-color-scheme, because there are times when it is nice to be able to switch on a site without having to change your OS color scheme.
While it does lack in many other areas, Safari on MacOS has a wonderful interface for per-site default behavior for: automatically using reader-mode, allowing permissions (microphone, etc), setting page zoom, etc. This would be the perfect place for per-site overrides of the system light/dark mode.