When I read it, I thought that the believers revered him as a God, or at least Quasi-God, that's why the 'your holiness'. But I think you theory is better
How? Enlighten me which part it is in the novel? I read it long time ago, so can't remember, the only thing I remember is that the emperor's name is "guy", there's no mention of his identity as pope have to get that part plss
So... I think there's a huge chance the one that take all those generations of emperors' body is... a pope...
Bcs they call him "your holiness" not "your majesty"