While writing my papers I try not to get bogged down too much. So if a paragraph doens't flow right I just type
TODO: rewrite on the line below it, and continue writing. When I think of something that I shouldn't forget, like an extra analysis to run I just write it down as a todo in the running text of my paper. I also write thoughts on my paper as a todo. Ideas on structure, whether I should maybe rearrange paragraphs or approach a subject differently, it all ends up as a todo in the running text.
When running the VSCode task for converting my paper to PDF (using Pandoc) it puts all the todos into the running text. That's fine by me, it helps as an extra reminder that stuff still needs to happen. But I wanted the todos to be visually different from the running text, so that it stands apart and doesn't confuse people who are reading my draft. That is where my Pandoc filter comes into play.