If I have git-started as a submodule at 3rd_party/git-started and I create a symlink from util/bin/setup_repository to 3rd_party/git-started/util/bin/setup_repository, then the script misbehaves. I believe it thinks it is being executed from within the git-started repository, thus it thinks it is not a submodule.
I am not sure if I can do anything about this behavior, but it is not desired and is thus a bug.