Annotations stored in the PDF file are read-only. You can still add those to Zotero notes, but if you want to edit them, you'll need to transfer them to Zotero from the PDF reader's File menu. Keeping annotations in the Zotero database allows for more advanced features (some existing, some still to come) and much smoother syncing/collaboration (e.g., the whole PDF doesn't have to be synced — possibly resulting in file conflicts — every time you edit an annotation).

(Note that Manage Attachments is from the ZotFile plugin. It might make sense to add an option to ZotFile to automatically trigger importing of embedded annotations when fetching a tablet PDF.)

it's a little bit unexpected that there's the option for automatically *extracting* annotations to a separate note, but none for *importing* them

Just to explain, this isn't an option because ZotFile doesn't know anything about Zotero annotations. The latest version no longer contains the manual Extract Annotations function specifically because it didn't work on Zotero annotations and was therefore causing a huge amount of confusion among Zotero beta users, whereas Zotero's built-in functionality works on both types of annotations. The get-from-tablet function wasn't changed, so that option will still run ZotFile's old annotation-extraction functionality. That option should really be updated to run Zotero's own annotation extraction instead, and whoever submits a patch for that (us, possibly) could add a second option to import the annotations.

@dstillman Unfortunately, it seems I'm still missing some crucial info. The notes I imported display as 'read-only' for other members of my team. What's more, their notes display as 'read-only' for me, and the option to 'Import annotations' is grayed out for them! What should we do to collaborate when dealing with a PDF, e.g. respond to one another's comments?

Thank you! I'm a new user so I didn't realize this was new functionality...