I think it depends. If the GUI tooling is exposing you less to the actual concepts and builds new concepts on top, that simplify things, then that will hamper a new user's understanding of the underlying concepts. Of course, it is not the CLI usage itself, that is the key here, but the usage of a tool, which exposes you to the actual concepts of git, and the most common tool like that is, of course, the default git command line interface.