I can reproduce your issue on my environment, it seems that OneNote does not support environment variable "%userprofile%" when setting default locations. Even I add the registry key "notebook root" directly as following image, it still does not work.
This issue does not occur with Word,
It's recommended to raise this issue to related Microsoft team.
To make this vocie louder, I have submited this issue in OneNote app.
Thanks for your understanding.
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