What makes you think there is a "rack full of legacy equipment", or that you're dealing with a "homogenized amalgamation of units"? You're just lining up straw men.
What multitude of devices does the Boxee Device replace that makes it an "all-in-one" device? It's one of many media streaming devices being released (though one based on very good software, granted), but all-in-one means it replaces a current multitude of devices. It does not.
I'd also like to point out that "literally" is not a term to be used when you want emphasis, the word you are looking for is "visually". Unless the device is a physical cube that you stab into the surface, it does not literally break the plane.
I think there are legitimate justifications for the design, if only that it needs to stand out in a market of plastic rectangles, but I don't think the reasons you gave are at all valid.