An average user is a myth. Every kind of average user has its own traits and they differ widely.
That's why there is such thing as system settings.
And yes, most desktop users are conscious when they work with files. Windows by default suggests "My Documents" folder as a target destination which is a pretty sane safe choice for all traits of average Joes.
Honestly I think not having a global filesystem makes things harder for the "average user." Most college students aren't going to only keep their word documents in word for example, they need to email them and upload them to tools like blackboard.
That's why there is such thing as system settings.
And yes, most desktop users are conscious when they work with files. Windows by default suggests "My Documents" folder as a target destination which is a pretty sane safe choice for all traits of average Joes.