We have done something like this in curvenote.com - as you mention, it is easier when it is a web-based service. Basically we just track the cell ID of a notebook (wherever it lives or is copied to) and have an extension that adds comments and version control as an overlay. Mostly people are using it to import/reuse figures into our notebook-like articles and keep the connection alive when you update the figure in Jupyter. Means not having to copy/paste, but instead having a live link with comments/versions.
Some of our users are also using it to reuse code snippets, or have different copies of a notebook tied together in certain by certain cells (e.g. simple plotting code). Still lots of kinks, but is certainly interesting to see how people use it when it is there.