At first, I thought that the sound was similar to an alarm being armed.
Another listen to the sound file in #1, but at a deduced playback speed lets me think that it could possibly be from the starter motor, in that it may still be receiving a signal to crank even though the engine has already started. Perhaps a sticky starter button or something along those lines.... However this is a wild guess on my part.
I would suggest removing the seat, with the bike out of gear, turning on the ignition, using a suitable tool to bridge the solenoid tags to get the starter motor to crank. See whether the noise is still there.