OK, time for the facts, such as there are. We explored this topic in painful detail some time back in the Tiger and Rocket forums, and even managed to debunk the urban legend about the EFI being the reason. (More on that at the end.)
The simple truth is largely what Street RRR's dealer said: it kills the engine, but not the electrics. We've seen people posting here time and time again who forgot to turn off the ignition switch afterward and ran their batteries down. Draining batteries all the way flat ages them prematurely, and they're awfully expensive these days.
There's a secondary factor involved: the kill switch is not really designed for continual use, on any bike. It MUST turn off the engine without fail any time you use the switch, and that is something it will indeed always do. But if that is done on a regular basis for too long, there's not going to be any guarantee the contacts will make good connection all the time when you actually want it
running. Now, as I say, this is a secondary consideration, and not something you need to worry about for
occasional use.
As for the safety angle...I wonder if the MSF have largely forgotten whatever the original reason was for their recommendation, and teach it simply because they always have. We keep hearing different explanations: so as not to have hands off the grips at any time while the bike is running (oh sure, everyone always follows
that plan

); or, to keep you in practice of reaching for that switch if an emergency does happen; etc. I suspect the real, original reason was that in "ancient times" (B.B., Before Batteries), the kill switch was sometimes the
only sure way of cutting the engine off. Even later, a lot of early bikes with battery electrics located the key switch poorly; you sometimes had to access very awkward spots indeed. Nowadays, our keys are about as easy to reach as it is possible to have them for routine use.
I can see a little merit in keeping the rider aware of the kill switch so its use is instinctive in an emergency. But I hardly think that requires daily practice. The only time I ever use the kill switch myself is on rare occasions when I have to park facing uphill, and I need both hands on the controls until the engine is stopped with the transmission in first gear. And guess what? I never have to think about where the switch is or fumble for it, even using it so seldom.
Finally, let's address the myth that using the kill switch will scramble the "brains" of the ECU. There is only an infinitessimal chance of this ever happening, if a highly unlikely series of failures were to occur at the same time. The reason is, the kill switch is in the
same line leading to the ECU as the ignition switch itself! It thus has the exact same effect on the computer as the ignition switch.
Here's what happens in normal startup and shutdown: When you turn on the ignition switch (with the kill switch in the operate position), 12 volts DC is applied to one of the two power inputs of the processor. It awakens quickly, and turns on the master power relay--which then supplies DC to the
other power connection on the engine management module. That's the one which the processor depends upon for its power the rest of the time the bike is running.
The startup/shutdown line (through the ignition switch and kill switch--and the alarm, if applicable) no longer sources significant current to the ECU...it now only serves as a user input to say, "yes, I still want the engine on." When you shut down, you interrupt that line with either the key or the emergency kill switch, but you're
not cutting off power to the processor! That's still sourced through the master power relay. You're only telling the processor it's time for the engine to stop, and therefore to quit sending pulses to the fuel injectors and the ignitors. So, the engine stops. But the processor keeps on working for a while, storing settings in memory, re-zeroing various stepper motors (the source of the "fax" sounds) so you won't have to wait for all that to happen during the next startup, and checking to see if coolant temperature is safe for the fan to be shut off yet. The ECU holds the master power relay engaged to keep itself turned on until its checklist is done. Then, it finally releases the relay and cuts off its own power.
I hope that clarifies things a bit.