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You've misunderstood. Permission Nanny has only one job: to work exactly like Runtime Permissions, but available on all Pre-M devices; instead of granting all the permissions at install time, the user grants individual permissions at run time. Users will still know when a 3rd party app wants to access your data because Permission Nanny will display a dialog asking the user to grant/deny access, just like M's Runtime Permissions, but on any device.
The integrated demo app may help clarify your doubts about Permission Nanny; users do not grant any permissions during install time, forcing the app to run with zero permission enabled. Instead, users choose to accept or reject individual permissions when the app is running.