Manuscript vs Working File
A manuscript is the text in the shape someone else expects to receive it: an agent, an editor, a typesetter, formatted to whatever convention that reader works in. A working file is something else entirely, the document a writer actually drafts and revises in, full of notes to self, alternate versions of a scene, comments, and structure that would mean nothing to anyone but the person who made it. The two can share every word and still be completely different objects, because one is written for an audience and the other is written for the process of getting there.
Where the confusion comes from
It's easy to treat the working file as if it already were the manuscript, especially once a draft feels finished. That skips a real step. A working file usually needs to shed things before it can become a manuscript: draft notes, bracketed reminders, an outline embedded at the top of the document, formatting habits that made sense while writing but not while reading. Calling the working file "the manuscript" too early tends to mean sending someone a document still full of the scaffolding meant only for its author.
How this shows up in a real novel
Mary Shelley's working notebooks for Frankenstein (1818), which survive today with Percy Shelley's handwriting visible in the margins, show a text still being actively built: crossed-out lines, alternate phrasings, edits layered on top of each other. What eventually reached the publisher as the manuscript proper was a fair copy made from that working material, cleaned of the visible back-and-forth that the notebooks still preserve. The notebooks are the working file. The fair copy is the manuscript.
While you're drafting
Keeping notes to self physically inside the working file, rather than in a separate document, tends to survive longer than any system that depends on remembering to move them somewhere else.
Questions
Is the working file just an early version of the manuscript? Not quite. A working file can include notes, alternate scenes, and structure meant only for the writer. A manuscript is a cleaned version meant for someone else to read.
When does a working file become a manuscript? Whenever it's prepared to be read by someone outside the process: formatted to their expectations and stripped of anything meant only for the writer's own use.
Should notes to self live in the manuscript? No. They belong in the working file, where they're useful while drafting, and should come out before the text becomes a manuscript meant for someone else.