My $0.02: Better to have a setting with a clear parent that is also incidentally accessed by something else, than a setting with no clear parent. If a script attempts to set the default, it should claim it with a prefix; if others want to access it, that's OK. That way every setting has a connection to the script that set it, and you have a chance in hell to figure out what it's for.
So basically, I'd recommend doing away with "common settings" and give them all a prefix - the script which created the setting.
(that's what I'm doing for my scripts, anyway!)