I have no friggin clue dude. That'd be my guess. when he's the Doctor, it might be JGL's real voice, and if it is then it has SOME alteration because of the breathing apparatus. I think it is his real voice for the most part, theres the unmasking scene and his voice changes slightly because he removes the breathing apparatus and I think JGL was really doing it with some slight changes to suit the way it would sound with the mask.
I actually ended up liking the Doctor's voice more and more although initially it was a bit WTF...but when he puts on the CC mask, it's DEFINITELY altered, no doubt about that. It's not that bad, I can grow to like it its just really inappropriate. Watch it and let me know what you think. I actually really liked the Doctor come to think of it. Ridiculous, creepy and sinister.