there's implications that things have been Weird with kris' soul for a while before chapter 1 starts. when you make that first save, the file is kris' file before it becomes the player's file. they maintained control until that point, until we took over.
they very clearly know what they're doing when it comes to the soul. they know how to maliciously comply and break free. they know how to take the soul out of themself and trap it. they know what the soul is capable enough to be wary of it.
the reason i wonder if there'll be a point when they take it too far is that they can't last forever without the soul. it slowly kills them to be without it, and as time goes by we see kris spending more and more time without the soul inside them. what if there's a point where they overestimate themself and almost die because of it?