In my newest game, William the Conqueror became PC, and within the week he had excommunicated me, a Welsh Count, and a Welsh 1-province bishopric too, which must have been for the lolz or something ("Look what I can do!"), since he never attacked him.
I don't believe that Popes are coded to get low prestige, it's just that bishoprics and archbishoprics don't tend to be very big, so they don't amass a lot of prestige before becoming Pope, they become Pope at a relatively old age so don't have a lot of time to get the prestige from being ruler of the Papal states either... which don't usually have that many titles, and hence prestige, either.
Also, I thought it was that the Pope needs to have more prestige than the target of excommunication has piety.
I think the Pope can only affect Catholics, Orthodox rulers at least can become excommunicated via events (church law ones?), but you'll also have to wait for the event to end excommunication to fire, there's no easy way to get rid of it, if becoming PC can be called easy. The AI doesn't seem to revoke excommunication, even if it was done by some long-dead PC.