I fail to see how this comes with the convenience of directory-specific symbolic links, dotfile-specific backups, individual removal & replacement of dotfiles, etc etc.

I've been using stow for years to manage my dotfiles and it's never been more involved than

$ stow dotfiles/urxvt

or what have you. In fact I would say that managing a git repository is more of a waste of time and far more over-engineered for a task easily solved by a tiny binary.

Not sure what you're referring to by an 'install script', have you ever used stow?

In any case, the real answer is that you should be using whatever works best for your use case, and for me that's stow.