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Interesting, but I think there are two drawbacks to this approach.
The first is already stated in the descritption:

"...This becomes challenging when the upstream sources change and
users themselves may maintain their own set of patches."

The second one is that it is difficult to contribute your comments
back. You would have to merge the comment files. A solution is to
maintain the comment file in the source repo, but then, if you have
write access to the repo you might as well add the comments directly
to the code.