noob question

You kind of have it, there is your home version of those folders that gets checked first, then a systemwide version that serves as a default.

Apart from defaults that are used when you run stuff under a new user account, there can be some duplication if you choose to install a program just for one user instead of systemwide. Not all installers offer that choice, but many do. Another place where this can happen is with fonts, different users will have different sets active.

 

they are what they are

OS X puts things where it needs them to be for the OS to work as designed. If you start monkeying around with certain items/folders, you could fubar your install and end up with a non-booting OS

best to just leave things alone, unless you are 100% certain of what you are doing.

 

Most definitely not. The Library at / level is the one for the full system and all users on it. the Library at ~/ is the User Library. If you're not the only user on the Mac, then deleting it from both automatically would mean that any other user who still wanted to use the app wouldn't be able to.

Incidentally, I wouldn't worry too much about random pref files being in your various Libraries. They're not taking up much space, they're not going to interfere with anything else and should you decide to reinstall the app in the future, your accounts/prefs will be set up.