I don't think there is really much benefit from adding that. In my opinion, notifications are there to inform you some action should be taken. Reputation and badges don't require any action.
According to this somewhat similar questionquestion about email notifications for badges and reputation, SE doesn't want to have an extensive list of options to toggle on and off, like you propose. That would mean this is a all or nothing implementation, and I don't think all users want such an option.