And you absolutely should be proud of your PDF->PNG->Highlight diffs script. As someone who has kept excel files and PDFs in version control I knew exactly the feeling you were talking about. I got to that part and exclaimed out loud, "Damn cool!"
Hot tip for handling office file formats or anything that uses a ZIP container: just unzip them and commit that to the repo. It won't fix the issue mentioned of the authoring tool making seemingly arbitrary and unnecessary changes, nor will it give you nifty visual diffs, but it's better than shuffling binary blobs through your version control tools.
Actually, it should (precisely _because_ of Git's approach to storing blobs) but that's besides the point. Saving space had nothing to do with the motivation for the earlier comment.
> in fact it will probably use more
No.