Hi I was having the same issue as OP but only found this post after making my own template. I’m no expert in nunjucks or Obsidian but this works well for my setup. There’s an image showing roughly what the output is.
Annotations from Zotero 6 internal pdf viewer are imported into an ### Annotations subheading, each annotation is nested inside of an admonition note (ad-note) for easy styling. Rectangle annotations will be pasted into the literature note inside their own block as images, as they are imported into your vault by the desktop connector. If you want to edit the callout (ad-note) blocks that’s easy enough by changing the values in the macro as per the admonition documentation. I find this easier than messing with the CSS options, for just certain files.
New annotations can be added to your literature note without fear of them overwriting the original file as there is a persist block for existing annotations. New annotations will be included under a separate heading with a new timestamp.
