Yep same. How does a bare repository make it simpler if you have to run a setup script anyway? A setup script can be as simple as this:

    #!/bin/sh
    mkdir -p ~/.config
    ln -sf ~/.dotfiles/vim ~/.vim
    ln -sf ~/.dotfiles/bashrc ~/.bashrc
    ln -sf ~/.dotfiles/gitconfig ~/.gitconfig
    ln -sf ~/.dotfiles/i3 ~/.config/i3

This is two steps instead of three. You can manage ~/.dotfiles like a normal git repository instead of the "dotfiles" command in the article. It isn't full of hidden files, you can put other scripts and stuff in it, you don't have to turn off showUntrackedFiles or add your whole home directory to gitignore, etc. It's so much simpler and easier to keep clean and organized. The only real downside is that to add a file you have to move it to ~/dotfiles and add a line for it to the script.

Side note, I get the benefit of publishing dotfiles for others to learn from, but why go through so much trouble to document how to install your dotfiles? Does anyone actually use the dotfiles of strangers? One time upon joining a company it was strongly recommended to me to just install another developer's dotfiles on my computer to get started. I had such a strong feeling of revulsion from this. Using someone else's dotfiles is like using someone else's toothbrush. I have my own, thanks.

It's good to look at others for ideas but for anyone new to versioning your dotfiles I would strongly recommend starting from scratch and doing the simplest thing that could possibly work. Hence a script like above.