Our usual procedure is to check individual mags at engine run up, then stop the engine by turning both mags off together.
Rotax engines do sound a bit solid when stopping....
Not having read all of the thread, I am probably repeating. But I do fly behind a 912UL - 80 hp, not an S.
I concur with the first part, I usually do it during taxi though some pilots religiously stop near the treshold to do it.
But I do not agree with the second part, exactly for the reason stated: cut one ignition, count three, cut the other. Engine stops much smoother.
@ShyTorque: the ignition on a Rotax does not use the traditional magneto's, but the dashboard switches still shortcircuit something or other to ground to disable it. If you want the full detail you'll have to find it, schematics are all over the www.