I dunno I feel like you're focusing on a detail that's not particularly relevant. The author's main thrust is precisely what you described about parsing changed files as ASTs.
It isn't relevant to the author's vision of content-aware diffing, but it is relevant to the author's complaints about how Git's (alleged) text-based-ness makes Git awkward to use with Jupyter notebooks. Has the author tried searching the web for "git diff jupyter"?
