AFAIK, although it was ages since I last tried something like this, all that's been disabled in-game is your ability to claim the title. If you mod in a claim, I think you should be able to pursue it as normal and, I believe, acquire the title using it.
Doing that won't cause any problems in itself. If you wanted to steal away with the military order titles then there'd be no problem. Problems might arise by claiming the Pope title because of how the Pope is used in-game by the Papal Controller.
Specifically, that might well mean that if your character, say, King of England is also the Pope and the Papal Controller is the King of Castile, then your prestige is going to be spent by one of your major rivals excommunicating any/all of his major rivals, which might well include you. Since this scenario was never planned for (ie, you're creating a situation that was never supposed to happen), you'll probably find it possible for the AI to force the Pope (you) to excommunicate yourself.
It'll also cause a few odd discrepancies when you try yourself for heresy or demand that you pay yourself indulgences for being sceptical (money which will magically vanish into thin air).
Personally, I don't think it'll add anything to the game to call yourself Pope. What would be fun, though, is to forcibly replace the Pope with your own chosen Pope and then keep an iron grip on the Papal Controllership for a century or so, which will give you all of the benefits of having the Pope on your side with none of the drawbacks associated with actually trying to be him yourself.
But, of course, its your call. Have fun.
