More likely, though, he said something unorthodox and that was enough to be deemed atheistic.

Agreed. If you look into the history of the term "atheism" throughout the centuries, it's a generic insult flung around at people whose beliefs or behavior you want to criticize. Popes have been called atheist on the grounds that if they behaved as badly as they did, they must not believe in a God who was going to punish them in the afterlife. This had nothing to do with a Pope preaching what we would call atheism today. ;)