The Amiga can change the bitplane data and colours as each horizontal line of the screen is drawn. That's how AmigaOS achieves that effect of multiple windows being drawn "in front" of each other - what you're really seeing is a lot of Copper instructions to change the bitplanes and colours as each of those windows is displayed.
That doesn't, however, mean that one window could have holes/transparency in it to display what's underneath, because the hardware can't work that way.