The use of one mag for starting is usually because that mag has an impulse coupling in it. This holds back the rotor against a spring until it suddenly flicks free, generating a strong spark. It only operates at low speed and also retards the ignition. This makes sure the cylinder is past top dead centre before the engine fires so it doesn't kick back and slice off your fingers (one reason I never hook my fingers over that nice sharp trailing edge). If you had both switched on you would have a risk of kick back from the non-retarded mag, and if it's electric start you stand a good chance of knackering the starter drive if that happens.
Interesting thought came to me the other day. We all switch each mag drop off in turn and are happy if we see a small (say <125) drop in RPM but how many of us would pick up on the dangers of getting no drop? Chances are it means that the mag didn't switch off and is permanently live. Stop the engine on the mixture, turn of the switch and you've still got a live mag.