Here's some info so everyone can decide for themselves whether or not to use the key, the handlebar run/stop switch, or the side stand switch:
When in the up position, the side stand switch on the Vee2 provides a ground path for the COIL of the side stand relay. It appears to carry no more load than a control circuit would. Also, this circuit is energized whenever the key is ON, so unless you are moving the side stand (in either direction) with the key OFF you are putting it under the same stress regardless of whether or not the engine is running. The side stand relay's contacts bear the load and stress of the "hot contact change of state" and they are cheap and easy to replace. The side stand switch's most probable cause for failure would be the ingress of crap since it is only a few inches off the road's surface.
Once the side stand relay coil is energized, power flows from the fuse through the relay's contacts to the RH Handlebar Run/Stop switch, then on to the low voltage side of all 4 ignition coils, there is also a shunt to the ECM (presumable to report the switch's status to ECM). The ground side of each coil goes directly to the EMC, so whatever load is there is being switched by the ECM internally when it wants the spark plugs to fire.
There may also be a shunt to the ABS module (I don't remember for sure), but that is probably also a control signal to tell the ABS module the switch's status. At any rate the high current parts of the ABS system have their own dedicated relays, so I doubt that the engine run/stop switch is carrying very much load in excess of the low voltage side of the coils.
As for startup and shutdown sequences... I don't see much of a shutdown sequence whether using the key, the engine run/start, or the side stand to kill the engine. I do however see the start up sequence repeated once all three of the above are restored to their run condition, regardless of which one is restored last.
Hope that helps...do as you will, it's your bike.