I guess my post was not clear. I am talking about using the Apple Pen anywhere you want.
For instance when I save a web page in Evernote, you cannot make any annotation on the page like you will do on a PDF.
Having annotations apart on another file and as a file attachment is not a way to work especially with other colleagues.
Today in order to manage my expectations I have to use 3 applications: Evernote, Nebo and PDF Expert.
It does not make my life easy...