SYSTEM is a special built-in privileged user, for example Services are often started from it. So the answer is no, other users aren't affected.
Currently trusted command lines and trusted users settings are system-wide, they have effect for all users. And program rules are user-wide, they can be different for different users. The best way to manage many users is to change default.rdb in RulesManager, this way these rules will be installed by default for any new user (and you can also install them for existing ones). So currently we don't have "All users" user, but maybe we'll add it, thanks for the suggestion.