>If the interface would be changed to conform better with the mental model of these users, surely it will conflict in some ways with the model of more experienced users.

I think it's tough to do, but certainly doable. What was outlined in the OP is just basic confusion amongst novices. Something that can easily be improved upon without hurting the experience for 'senior' users. I imagine this is how Mac does it. They throw their software up against the shores of a million and one newbies and iterate until they have a product that they are happy with. Testing is an integral component of UI design & creation, and from the looks of it, Ubuntu is slacking.