I don't find it that amusing. Do you think God only works through those that have 100% correct doctrinal beliefs?
God worked through the pagan prophet Balaam. God worked through the three wise men who studied stars. God worked through the Medium that Saul consulted. God worked through Satan's attack on Joseph in selling him into slavery. God worked through the men who had Daniel thrown into the lion's den.
To say that God may have given us additional insight into the end time through a prophecy about the popes, is not necessarily an endorsement of Catholic traditions over protestant. To say that God used Malachy to deliver that prophecy is not necessarily an endorsement of everything Malachy believed.
A long time ago, probably 20 years, I had a dream in which a voice said "The two old men are not dead yet". I understood that dream to mean the End Times would follow. And I understood the two old men to be the Pope and Billy Graham. I've watched with interest over the years as the press has focused on those two as the most prominent leaders. Even during the death of Pope John Paul II, they had Franklin Graham on and was asking him about the health of his father. Was that dream prophecy or just a dream. I don't know. But all of the other signs say we are close.