I think what you've said is all correct. And its mimicked, to some degree, by how we build our physical lives. Shelves and desks are not so deep as to obscure what you need.

That said, I think an element that's missed is tangibility. In the real world, a stack of papers and folders are a valid way organize your own desk. You know where everything is and allowing you to tune your layout and grow muscle memory is very helpful. VR interfaces should let the user organize as they see fit. Interfaces should be tangible, movable, sizable, etc.