The ECM saves idle setting info each time it powers down, whether you use the kill switch first or just the ignition switch. Where that subject came up was with the early electronic throttle bikes, where if you didn't let the throttle return to idle before switching off, the bike would idle high when you next started it. I and others recommended at the time that people take their hand off the grip and turn the bike off with the ignition switch, to avoid accidentally holding the throttle open.
I very rarely use the kill switch, and have never had a single problem related to that fact. It exists for one reason only, safety. With the ignition switch on many bikes located in spots that aren't that easily accessible in an emergency situation without removing your hands from the controls, it made sense to have a kill switch on the bars. It has always been my opinion that Harley recommended shutting down with that switch just to get people used to using it, so when an emergency occurred it would be easier for the rider to quickly react.
Jerry