Hi Kevin,
What kind of policies? You mean stuff like proxy configuration?
The Android security model disallows one app from reading/writing another app's data (which is what it sounds like you're trying to do). Also, even if that were possible directly messing with configuration files sounds like a terrible idea - how are you going to deal with different versions or Chrome and your app writing at the same time?
It sounds like this would need to be something Chrome itself exposes support for (perhaps by means of an Intent or Binder) that your app can invoke/use to deliver the functionality you want.