We take a very different approach with VersionPress which puts nearly everything in the repository, including core files, all the plugins, themes and the "database" (actually a mirror of it in a Git-friendly format). If you're just a user of such site, this has a major benefit that you only need the repo to reconstruct anything and everything from the site's history, without the dependency on any external tool or workflow. It is, in a sense, a perfect backup with all the nice version control features added on top of it. The downsides are relatively minor, mainly the larger repo size but it's usually not that bad and well worth the benefits.

Another story is if you are also a developer of one or more of the plugins or the theme, and even more so if they are used on more WP sites of yours. In that case I agree that making a separate Git repo for each of them makes sense and we do that e.g. for our blog site which is VersionPress-backed but the theme lives in its own repo.

These approaches are not mutually exclusive and I think both of them make sense and are useful in their own right. The article seems to focus only on the latter scenario but it's late at night here and I might have misunderstood something..