Remember how he says "Maybe you three can break your own strings.""

What if WE, the player (Canonically someTHING else, not a player), are controlling Kris' soul? When they rips it out we loose sight of them. After they rip their soul out in CH2 they crawl outside through the window but the camera doesn't follow them. They put their soul back and the camera follows them once again. This could just be toby trying to keep some surprise away from us, or it could be something important (This is just something I thought of when I was trying to fall asleep last night). What if Kris makes the dark fountain at the end of CH2 because they doesn't want to be controlled anymore? They want to make a choice of their own, remember they turn toward the camera at the end of ch1. Also bring back the line "You don't choose who you are in this world." to your mind. That's could support this crazy, sleepless theory I had.