The instructions I've seen have always said not to brake to a complete stop, just brake hard to a low speed, then repeat a dozen or so times. It's more about generating heat in your brakes to transfer pad material to the rotors than about the speed you use to get there. I don't get too worked up over the process, as I haven't found that much of a difference in braking afterward and the pads will bed in from use, anyway. Also, the first time your brakes get wet, you'll have to do it all over again.
I think Magura's instructions are more appropriate for a downhill MTB than a gravel bike.