Every guide to atomic notes eventually meets the same objection: most of what I write cannot be atomic. A meeting note is a list of actions and a transcript of a specific day. It’s an event. A project plan is a spec file that contains decisions and at times, serialized tasks, glued together. I do think if a system demands everything become atomic, that system quickly becomes useless.
In Sönke Ahrens’ description of the Zettelkasten workflow, permanent atomic notes are the output of a pipeline, not the only format allowed to exist. The original system never demanded that.
Fleeting notes capture and source-bound notes feed the pipeline and remain themselves. They are only as useful till I reach the output. This is why the kind of note file should live inside different folders. They have different life cycles.