Speaking as an App Developer, we cannot touch stuff like that. We're allowed to ask Touch ID to verify things and process the results, but we don't actually get to use the Touch ID system. It's similar to how the shared keychain is used: We can ask iOS to do things, but then must handle any one of many possible answers. We don't actually see your fingerprint in any way.
Now Cydia and 3rd party stuff? I have no clue.