Maybe not the answer you’re looking for since I’m very new to this sort of app and very unskilled overall, but I think the PDF annotations button is a self-created page to store or the highlights you make on that PDF, you can add your own notes or comments there as well.
If you take your notes on the right, most likely in the journal I guess, you have to manually copy and paste the references in the journal, then you add your notes or comments down below.
I guess the annotation button allows you to make highlights and comments without having the need of creating an additional dedicated page for that, which is something that I was actually planning on doing before realizing I just could do that right there in the journal down below the asset.
BTW do you guys know the difference between Copy reference and Linked reference when making a highlight on a PDF file?