The pencil isn't very smart..

[Krevnik]

i also think the pen on the surface would just be used as a stylus in apps that didn't explicitly use it. Pressing the buttons on the pen would act as left/right click.

And lo and behold, that's exactly what the pencil does. In apps that don't explicitly do anything with the stylus touch type, they act like it is a finger (since if you do nothing, that's exactly what it looks like to the app).

Now, if you want to disable finger input, that's up to the app. With palm rejection, I see no need in something like notes to actually have a toggle that you have to fiddle with.