Sometimes you may need to alter a template that is provided by a module. Usually, you will be able to override the template by copy it into your themes template directory.
But in a case such as Drupal multi-site setup with a single code base and shared the theme, it is difficult to alter template specifically for a particular website. Then if you are doing it using a module you will be able to achieve for a particular website.
The hook hook_theme_registry_alter() will help to alter the template path for a particular theme function.