Calls to GetLoginItemSettings (amonst others) will get GetAppUserModelId which will implicit set a new one if there hasn't been a user defined one yet.  This causes an issue in a UWP environment where the AppUserModelId is system defined.

On the latest versions of windows the AppUserModelId defined for your notification must match exactly the one defined for your process or no notification will appear.  Got a fix in the works for this just raising here for tracking purposes.
atom/browser/browser.h
bool OpenFile(const std::string& file_path);
  
  void OpenURL(const std::string& url);
#if defined(OS_MACOSX)
  
  void NewWindowForTab();
#endif  
  
  
  void Activate(bool has_visible_windows);
  
  void WillFinishLaunching();
  void DidFinishLaunching(const base::DictionaryValue& launch_info);
  void OnAccessibilitySupportChanged();
  
  void RequestLogin(LoginHandler* login_handler,
                    std::unique_ptr<base::DictionaryValue> request_details);
  void PreMainMessageLoopRun();
  void AddObserver(BrowserObserver* obs) {
    observers_.AddObserver(obs);
  }
  void RemoveObserver(BrowserObserver* obs) {
    observers_.RemoveObserver(obs);
  }
  bool is_shutting_down() const { return is_shutdown_; }
  bool is_quiting() const { return is_quiting_; }
  bool is_ready() const { return is_ready_; }
 protected:
  
  std::string GetExecutableFileVersion() const;