On my previous bike, a 2005 Yamaha FZ6, I used the kill switch first and then turned off the key practically every time I turned off the bike--twice a day--for years and never had a problem. Then I bought my 2013 Triumph and have been doing the same thing for about month now with no adverse affects. I actually get into neutral, flip the switch, and then coast into my parking space at work. Then I turn off the key. No problems here.
Well okay, there is one thing that is odd and shutting down this way might be causing it now that people are mentioning that the manual suggests using the key: Sometimes my alarm light will come on when I turn the key to start the bike and it won't start. I can't remember if I flipped the kill switch back on before I turn the key or vice-versa when it does this. I have to turn everything off and on and it usually is fine for the second try. I'll have to try some scenarios and determine what makes it happen. Otherwise, the bike runs fine.