I see this so often with power user tools. All power user tools are tools that you can only use reasonably well with some basic understanding. They are made not to be understood in the easiest fashion but to handle all complexities of a problemset as efficiently as possible. Therefore it sometimes seems harder to use from the outside, but actually the hardness comes from the problem it solves, not the tool.

So yeah, if you really want to use git well, learn its internals. It takes some time but actually not even hard. After reading the Git Book once I was even able to implement my own git (of course without performance considerations).