I know for many years OneNote files have been hidden by default because they wouldn't download as per onedrive: Ignore OneNote links · Issue #211 · rclone/rclone · GitHub but OneNote files do download now and don't throw any errors in rclone. They seem to open fine in OneNote 2016/Desktop version (although I haven't had the same luck with the mac version).
This appears to be quite a recent change change as in my memory it has never worked and this Reddit post
from a year ago seems to be running into the same error I am used to.
I am using an organisational Microsoft account and it appears to work with your personal notebooks, copied notebooks and OneNotes in sharepoint sites too. To replicate this the config needs to be updated with expose_onenote_files = true. I am using rclone v1.70.2
I suggest that the default behaviour be changed as many people might want to backup their OneNote and the download button still does not appear on OneNote. If not, I suggest the --expose-onenote-files part of the documentation to be updated to reflect this change.