Customary Marriage: After the customary rites of marriage are performed, the couple can register at the local Registrar of Marriages in the district where they reside, along with one witness. They will be asked to provide a statutory declaration describing the marriage ceremony and declaring it was made in accordance with their ethnic group’s customary law. The application for the registration of the marriage must be made within three months of the marriage ceremony. The certificate will say "married under customary law" in the space provided for "condition."
So assuming that has not been done your Mother can file for her, you do not file for the children.
I think it is safer that your Mother naturalises as then the question would be is it F1 or F3 not is she was petitioned at all.
She only files for the Daughter, the newborn would be a derivative.
You should also file for your sister, her being married or not is not a factor for your petition.