I must admit that I do not like the concept of reading/editing of pdf’s inside of apple notes (new macOS Sonoma feature). I feel very comfortable with apples preview app or its epub reader. So opening a file in these apps from bear is at least in my eyes an ideal solution.
However, I miss the feature to show the highlights and comments of a linked pdf inside of bear. I thought that this cannot be realizable in bear because the highlights/comments inside a pdf always can be changed and that would require also to change automatically the excerpts within the note. Also the questions would arise what to do if you manually edit these excerpts.
I had the idea about a special preview for pdf’s that offer a foldable textbox that spans nearly the whole text width of the editor and holds the non-editable read-out excerpts from the pdf. As I have neither the tools nor the skills to generate a nice mockup, here an ugly manual sketch to show what I mean. Enjoy! 
