Users currently look at the 64GB number as a rough approximation of how much music/files/apps they can store on that device. Maybe they are wrong to do that, but that's the current intuitive assumption for Jane Doe buying an iPod. So with that assumption, they are certainly not getting what the box tells them.

The answer could be to e.g. publish a "usable space" amount on the box. Basically, to eliminate this misconception/miscommunication from the customer's mind.