Here is my list of pros and cons on the matter (taken from the user manual, §18.1, Inline vs Linked):
Lots of them...
Which of these to use will remain up to you and your preferences in most cases. You might even find that a mixture of methods will suit you, using inline notation for short comments to yourself about prose, and linked notes for other types of comments.
There are a few advantages and disadvantages to each method:
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Inline notes are always visible in your text; there is no way to diminish their prominence. So for some forms of notation, this can be an advantage in that you cannot defer or easily ignore them. This also makes it easier to see your notes and your book at the same reading speed—there is no need to look off to the side to get a feel for the “meta” book.
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Linked notes do not disturb the flow of text, no matter how large they may be. This means even the lengthiest of notes can be placed into your text without having to scan from word to word in order to read the underlying book text.
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Inline notes, being within the text itself, do not require any additional interface to use and never require the mouse to read. They thus work well with a slim workflow, or in situations where screen space is at a premium.
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Linked notes can act like bookmarks. Clicking on them in the inspector will whisk you right to the spot in the text where they are anchored.
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Inline notes can be placed anywhere you like (especially annotations), even in between paragraphs or at the very beginning or end of a section, whereas linked notes require something to “anchor to”. This makes inline notation more useful when jotting down notes in sections before you’ve even started to write.
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Linked notes can be easily viewed together in a collected interface no matter how far they are spread apart in the document. This becomes especially advantageous in a Scrivenings session. A note on page 10 has the same prominence as a note on page 1.
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It follows then that inline notes are only visible in the current contextual surroundings. Notes that are pages away, and do not presently concern you in your writing and editing, are hidden by the same virtue that hides these irrelevant texts from you: the sheer bulk of your words.
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Inline notes exist around your text and do not depend upon it to exist. This means you can edit the text that the note refers to freely, without worrying about losing your comments. This is in opposition to linked notes, which are anchored to the text—if the text is removed or entirely altered, the note will be deleted.
By corollary, inline note quantities can exceed the textual capacity of the base text. For most authors this will not become an issue, but in some fields, such as qualitative data analysis, where the amount of annotation can exceed the original text, running out of suitable anchor text could become a problem with linked notes. Inline notes, being unanchored, have no limits.
These are just a few examples, and hopefully that gives you an idea of the individual unique merits in these approaches. The next few sections will address each of these types in more depth.
Speaking for myself, I’m in alignment with the last few posts. I’ve never been too keen on the concept of keeping working notes in separate little bubbles or boxes. If something in the text is broken and I need to fix it, that’s just as important to me as the text itself, maybe even more so. If one is going to think of inline notes as clutter, that’s the kind of clutter you want. It’s putting the trash bag in front of the front door so you remember to take it out instead of festering in a sidebar for months. But, as I note in the list, there are definitely things comments are very good at, like setting arbitrary scroll points. I mark figures, tables and other notable info-dense objects with comments, precisely for that reason.
While I’m at it, I might as well link to some thoughts on the larger topic. There isn’t much new in there, from what I’ve skimmed of the above, save perhaps for some process-design-level remarks on the notion of collapsing legacy habits into a system that can take it. I.e. why use a separate spreadsheet to track your book data when you have a program like Scrivener that can embed all or most of that kind of data into its Outliner? Why maintain a discrete checklist oriented approach when the software can embed what we need to do right into the content itself and provide said checklists dynamically with its search features? Maybe there are good reasons, don’t get me wrong, but I think the question should be asked at the top: can I do this without building a formal to-do list tracker into the software? Can I get away with a collection looking for text markers or some other low-impact / high-reward system?
Here is another approach, which embeds a lot of these smaller pieces into a cohesive system. It is not as narrow as only applying to tracking todos (which often can be forgotten about once done), but is very adjacent in the sense that it attempts to address what needs to be done, where the process of doing these things is important to document; to have what has changed become a long term record of changes, with as much detail as you need (down to what Snapshots-compare can tell you). It’s a bit more overhead than just adding and deleting inline notation markers, for sure, but if you need to know what you fixed in five years, you will want more than that anyway.