Stopping an engine with ICO assures that no fuel is left to burn as the engine slows to a stop. If there are glowing deposits in the cylinders, and you have shut down by turning the mags off, the continued flow of fuel into the combustion chambers can be ignited by the glowing deposits, and cause a backfire. Such backfire or run on can be unsafe, when you simply want the propeller to stop, and can be damaging to the exhaust, if that is where it occurs.
To a lesser degree, the now flooded engine can be more difficult to restart, if you want to do that right away.
I too have flown aircraft which had to be shut off with the mags, for lack of a mixture control, in which case you obviously have no choice.