When specifying a 640x480 windowed mode, Dolphin should create a 640x480 drawing area and create a window frame over that area, not create a 640x480 window with a smaller drawing area leading to a lower than specified resolution and vertical black borders:
In this case, the window size should be 650x512 for true 640x480 graphics.
In this case, the window size should be 650x512 for true 640x480 graphics.