Personally, I wouldn't conflate the (module) installation and (application) setup steps. Especially adding interactive parts to the module installation will wreck your chances of automated installation of the module.

If the module can use some general information, I would add another script to the module which asks the user about some information and then fills a hardcoded template using that information. That way, you can easily add comments and optional (commented out) sections to the user configuration file without needing special handling.