Ending and 100% question


I know there was talk at some point of Penn's quest influencing the ending - I don't entirely remember what I chose during that quest but maybe friendship, given the ending I got. Does choosing this make it impossible to 100% the game? I'm at 99% right now; I've gotten the item from mana's dog and the guard lady. Is there anything I'm missing? I was at 100% before the .99 patch I believe.