Part of the reason for using the fake fullscreen mode is with multiple monitors, but it can be useful with one, as well. For example, certain mouse options in Windows, or conflicts with certain programs, can cause the mouse cursor not to show up in fullscreen mode, but it may be ok in a windowed mode.
Someone recording or streaming a play session may get better results in a windowed mode than running it fullscreen.
SteamOS is a customized version of Linux that Valve released, optimized specifically for gaming.