I'd think the opposite; if you were combining hfs and non-hfs at a visible level, the way to do it would be to have a non-hierarchical storage system underneath with superficial hierarchical (and other) views. This would give you the flexibility to change your schema without breaking file paths while still being able to organize and name things sanely.
As far as metaphors, I'd say think of calling someone on a landline vs. a cell phone. With the cell, you don't have to specify where or who joe is (/people/friends/joe/house|work|carphone|vacation|etc.) in order to reach him since joe's 1 cellphone number rings wherever he happens to be.
Another example is folders on the iphone -- moving an app into a folder with other apps doesn't actually move the app from /homescreen/app1 to /homescreen/games/app1 on the iphone hard disk (as far as I know...), it just changes the superficial hierarchical view of the data.
As far as metaphors, I'd say think of calling someone on a landline vs. a cell phone. With the cell, you don't have to specify where or who joe is (/people/friends/joe/house|work|carphone|vacation|etc.) in order to reach him since joe's 1 cellphone number rings wherever he happens to be.
Another example is folders on the iphone -- moving an app into a folder with other apps doesn't actually move the app from /homescreen/app1 to /homescreen/games/app1 on the iphone hard disk (as far as I know...), it just changes the superficial hierarchical view of the data.