At first, because it was different and didn't fit into my current patterns of use for Logos, I hated the fact that my note files were getting cluttered with notes from my markups.
Knowing that this is happening, I'm starting to like the potential here. I like that I can create a note file are a particular study of and mark a text of the Bible up like crazy without worrying that I'm going to see it later (Or I can annotate what the heck I meant by what I was highlighting)...I just hide that note file in the future.
Or, my wife can have her quiet time note file open and markup the Bible during her Bible reading. I then open my quiet time note file during my reading and our markups are separate.
Alternatively, I can create a new note file for a particular book I'm reading and then in one place I have easy access to all notes and highlights from that book. (REQUEST: I do wish that the entire highlighted quote appeared in the note file rather than just the "beginning...end" excerpt. This would allow this new feature to function more like Kindle's feature where I can browse my highlights).
Finally, I really like that I can change the highlighting style from the note file without having to delete the old highlight and then re-do it.