That emperor, through this pope, said that what the Prophet Muhammad brought to the world was "only evil and inhuman, such as his command to spread by the sword the faith he preached." Like Christians often did? The pope did not mention that.
Of course, it would have been off-topic if he had — as Marty seems to acknowledge himself.
The greatest loss here — well, with the possible exceptions of the victims of the violence of Middle Eastern drama queens — is that the Pope's central pro-reason thrust seems to have been utterly missed.