In my point of view, you cannot separate "the way you use the tool" with the "tool itself". A hammmer is easy and straightforward to use because of its design features. That is what makes the hammer useful. Granted that there are complicated tools, that require a steep learning curve (a pipe organ, for instance), but that should not be the case of git.
The whole point is that the tool should make it easy for you to do what you intend to do. That's the whole point of criticizing an application (or tool, as you put it). I am pretty sure that you can make beautiful and exact things with Git, but the fact is that sometimes they are difficult to perform or counter-intuitive, and that's the crux of the criticism.
A tool should not be designed only to "allow" people to do certain things. It should also make these things easy and straight forward.
It's impressive how (most of the times) our usage of a tool is directly linked to how it was designed. Therefore, design features (like the ones proposed in the article) cannot be distinguished from the "core" of the tool, or the functionalities it allows one to perform. The design, in some sort of way, is the tool. And that's what conditions our usage of it.