In order to skip the extra step of adding or staging files, I often use Commit Selected. However, this option is not allowed when the only selected item is a reference to a submodule commit.
To reproduce:
1. Add a submodule within the outer repository.
2. Open the submodule, change a file, and commit the change.
3. In the outer project, select the submodule's "file". The Commit Selected button and menu entry are disabled.