This is exactly what I was getting at. git's command layer is much like the "new" keyword in Javascript -- it's a false abstraction of a relatively elegant underlying system [1]. As it is, the command layer encourages a naive mental model that is both inaccurate and leaky. You end up having to learn both the abstraction layer and the actual system underneath in order to actually understand what any of the commands do.

[1] I assume this was originally done to make git seem more approachable to SVN or CVS users.