During live play, that flashing, red light indicates that a fill will be coming on the next beat, even when you do not select a new variation. When you select a new variation, and if the auto-fill it activated, it will select the fill from the newly selected variation. If the auto-fill is turned off, only a shortened fill is produced when you change to a new variation, however, if that same variation button is pressed again, you will get the full fill of that variation.
I know this may sound a bit complicated, but by working with it a bit, you will quickly see the benefits,
Gary