WP Codex says that it is recommended to register all meta fields with register_meta() function.
I see no reason why it couldn’t be implemented in ACF. It won’t break the backwards compatibility but it would give ACF users more control over custom fields. For example register_meta() makes it super easy to expose custom fields via REST API.
Additionally, it gives some interesting, advanced features like auth_callback and sanitize_callback which are “hookable” via sanitize_{$object_type}_meta_{$meta_key} and auth_{$object_type}_meta_{$meta_key} hooks
