We haven't tested the Pencil, so I don't have a definitive answer for you (yet).
I would guess that it will do a fine job of PDF annotation as that function is currently available in SmartOffice 2 for all devices, and the pencil should allow for more precise free hand drawing than using your finger.
For Word documents, my guess is that the pencil would not offer free hand annotation or text entry within the document.
You raise a good question though, and we'll pick up an Apple Pencil and test it with the iPad Pro.
Thanks for asking the question.