Serenity Caldwell for iMore:

Apple’s pressure-sensitive tool is incredible for drawing and writing on the iPad Pro’s screen, but its navigational ability is just as important.

In my opinion, part of the iPad’s magic is the physical contact of your fingers and the objects on the screen. I remember using the device for the first time and feeling more connected to it than any laptop or other mobile device i’d previously used.

I don’t have a ton of experience using the Pencil, or I don’t understand the context, but I don’t want to be able to use the pencil for navigation. As John Gruber says in his commentary on the subject, this should be a toggle in the settings much like the mute/screen rotation lock if people are that passionate about it.