Dotfile management this way--how to support machine-specific dotfiles?

Do you use git pull or git pull -r? I'm having a problem with subsequent git rebase master after the initial when one when I created the repo. I'm following this method of dotfile management (and this one as well). I made a thread here and I would really appreciate it if you would take a quick look to see if your workflow is different from mine and/or what problem I'm experiencing.

Much appreciated.

/r/archlinux Thread Parent