Some of these issues were addressed in my reply to another post. An empty table can be given with {independent_variables: [], dependent_variables: []} and then attach the YAML file as additional_resources.
hepdata_lib has separate documentation at https://hepdata-lib.readthedocs.io but indeed I don’t see an example of how to use the add_additional_resource function. I’ll raise the issue with the hepdata_lib developers. But the add_additional_resource function can be called as a method of instances of either the Submission or Table classes. So you would call something like table = Table("Table name"), then table.add_additional_resource("description", "path_to_file", copy_file=True) and don’t add any Variable objects to the table. I think that would meet your needs.