Is there anything actually better about OneNote 2016 vs. 2013?
I usually use 2013 over the app, since there are some features missing (e.g. handwriting recognition) in the app.
As for how to do it, just open the "Surface" app that comes installed on the SP4. After one of the recent updates, there was an added tab in the app that lets you select which app the eraser button opens.