Convenient Way to Turn an Apple Note to EPUB
Sorry you had challenges with the copy to pages. In my experience, the content from the note to Pages is generally excellent and one step. Pages has EPUB export capabilities and it will take over all function for authoring from iBooks Author in the next OS release cycle in 2020.

https://support.apple.com/en-us/HT211136

I think you will find the hassle to get it into pages lessened over time and benefit from having it in a format you can edit easier than PDF.