But seriously, the fact that there is a .gitmodules file lulls you into a sense that that file is "the configuration file". If you don't know about these other files, then it's natural to edit .gitmodules. When you make errors, the fixing those errors are pretty hard. There is no "git submodule remove x" or "git submodule set-url" or "git submodule mv".

For example, do you know how, on the top of your head, to get an existing submodule to track a branch?

How do you think someone who does not quite understand git would do it? Even with a pretty ok understanding of git infernal, you can put yourself deep in the gutter. (case in point, if you enter the submodule directory and push head to a new commit, you can just "git add submodule-directory" to get point the submodule to the new commit. But if you were to change upstream url or branch or something else in the submodule, you're screwed. That's not intuitive by a long shot)

Edit: git submodule sync is not enough by the way... You can fuck up your repo like crazy even if you sync the two configuration files.