IO, I assume that because your machine is injected, then the procedure may be different, but I still wouldn't recommend switching the mags off totally and can't really see how it would be totally different anyway.
Mind you, I still hate the idea of magnetos compared to a proper electronic ignition system!
The cynical part of me wonders if the engine manufacturers want us to dead cut, so that their aftermarket parts business gets a boost! How much is an new 540?