Francis didn't say that God "allowed" or "permitted" all religions. Instead, he said that God "willed" all religions.
A Filipino priest did the same thing 3 years ago and he was suspended.
The pope's statements were from conversations between him and the book author in AUGUST at the Vatican - most likely after the McCarrick scandal broke out but before Vigano's revelations came out implicating the pope of coverup. After Vigano's revelations, I don't think the pope even wants to talk about homosexuality in the clergy anymore.