The quoted decrees refer to "of Austria-Este" as a surname. I would say that "of Austria" was considered the surname aad Archduke/Archduchess was considered the title, comparable to other German dynasties.
so daß Seine k. und k. Hoheit und Höchstdessen auf Grund der Primogenitur-Erbfolge nächstberufenen Nachkommen aus ebenbürtiger Ehe den Namen Österreich-Este führen und das estensiche mit dem eigenen Wappen vereinigen werden.
(so that HI&RH and those of his issue from equal marriage called after him by primogeniture shall [ bear the name Austria-Este and join the arms of Este with their own.)
Do you have an example of Habsburg-Lothringen being used as a legal surname prior to the end of the monarchy?