As per DC42 comment, I have added a 5K resistor between the pin (exp.e3stop) and GND and my issue is solved - the voltage spike at startup/shutdown is minimized and the pin can be used to send signals to an Arduino during operation without hazard of stray signal being send from reboot.
Best posts made by vasparshin
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RE: 3.2 Servo making a grinding noise on reboot/M999posted in Beta Firmware