In Obsidian, for example, you can choose where your media data is stored (and there are options to store them alongside the Markdown files, e.g. in a hidden fol

In Obsidian, for example, you can choose where your media data is stored (and there are options to store them alongside the Markdown files, e.g. in a hidden folder). I guess OP’s point is that this would be a better way, or at least to store media in the same root folder as notes and not some arbitrary folder far away from the notes.