The 2009 apology was made personally to Phil Fontaine, not to all residential school survivors. From the article:
"In 2009, Pope Benedict offered a personal apology to Phil Fontaine, a residential school survivor and Grand Chief of the Assembly of First Nations. That apology was not accepted by the commission because it was not offered to all victims of residential schools."
Trudeau has already called Andrew Scheer from Italy to congratulate him.