The electrical wizards say the key switch is bound to have a tiny arc each time the switch is cycled and it's best to use the kill switch before the ignition is turned off, and after it's turned on. The ignition switch would be protected from any electrical surges.
After hearing all of the problems with the ignition switch on the FJR1300, I'm suprised I haven't seen someone mention this before in this forum.
In at least one thread here someone actually mentions jiggling the ignition switch to clean the contacts. The contacts get "dirty" possibly because there is a slight arc when the circuit is interrupted with the key switch. Even though the switch is probably mostly just turning on relays, there's still current interupted (by the ignition switch) when you use the key.
I happen to be one of those MSF instructors who teaches people to use the kill switch. I can't tell you how many times I've had stubborn students complain that there was something wrong with their bike and the problem turns out to be they weren't following the process that we teach (to shut down/start up).