Is what is mentioned in "Khazain al-Asrar" concerning a specific way of performing a rak'ah after the Witr prayer, involving the recitation of "Subbuh Quddus" and Ayatul Kursi, and the great reward that follows, authentic or an innovation (bid'ah)?

What you have read is incorrect and contrary to the guidance of the Messenger (peace be upon him). There are no two Witr prayers in one night, and reading the Quran after rising from bowing (ruku') has not been established; it is an innovated bid'ah. We advise you to disregard this book.