Yeah, I'm pretty sure that the in-game counter removes time looking at cutscenes/menu screens. And I'm 99% sure that it doesn't count replays of days. I beat the game in 44 days in "11 hours", and someone else beat the game in 55 days and also at "11 hours". I haven't checked the activity log yet, though. Kinda strange, because each in-game day takes the same amount of time.