You are exactly right on both counts... I remember when Microsoft released the very first version of OneNote. While they obviously knew what it was, they completely failed at explaining to us why we needed/wanted it. As such, not many of us did. I evaluated it and was pretty much "meh...".
It was until Evernote came along that I really saw the potential for these applications.
And your last point about how Microsoft would experience minimal impact if OneNote simply disappeared is exactly why I would never go all-in with OneNote. It's been around so long that I doubt it will go anywhere soon, but there's no guarantee the next CEO or product manager hired doesn't decide otherwise.
Evernote can't live without Evernote, so as long as they don't run the business into bankruptcy, I feel my data is safe.