Your implication that they haven't considered the effect on users is patently ridiculous. Everyone who knows a little about UI design is aware that guidelines and research results are an input to the design process, not an output.
The change, I think is a positive one, for a number of reasons. First, remember that the previous in-place method had problems: it was non-obvious how to easily drag and drop stuff between places; it took longer to identify the folder a window is showing (it's a lot easier to identify something if its general shape is different); such a scheme is still not very usable for navigating large hierarchies.
Studies have shown that the target user market do not cope well with deep, complex hierarchies anyway. The new scheme has some obvious advantages for shallow hierarchies: "ah, my spreadsheets folder is here, just where I left it". Bear in mind the eventual impact of the Storage project, too.
The minority of users that can handle complex hierarchies with ease still have an easily available switch to use.
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