I recall my owners manual says not to use the kill switch except in an emergency.
I use the key.
The manual does indeed state that leaving the ignition "on" whilst the engine is not running may result in "electrical damage". This doesn't explain what is happening from the time you turn the key to "on" and when you hit the starter. It would follow that the time you hit the kill switch to turning the key to "off" is comparable.
If there is a special routine that the ECU performs on shutdown, it would have been engineered (Japanese I am guessing, not Pommy) into both a key shutdown or a kill shutdown.
Leaving the key in the "on" position for an extended time is an obvious mistake, probably related to battery drain and how that may effect the ECU whilst it is lit up.
I think the most important thing to mention here is the routine we all use to start and stop our bikes. The routine is meant to prevent mistakes like side stand up drops, battery drains and ECU problems (and in the old days leaving the petcock open). So the routine we each use, works for us individually. If you have made the aforementioned mistakes then maybe a routine would be helpful. This is why there is a routine taught in the professional courses.
Similar to starting an airplane, the routine may have a left-to-right habit or an acronym like FINE-C* to start and right-to-left pattern: T(humb [kill switch]) K(ey) F(uel) to stop.
*
- Fuel (gotta turn that fuel switch back on, if you have one)
- Ignition (key)
- Neutral
- Engine cut off switch ("kill" switch)
- Choke and clutch