The blink patterns you linked to are being controlled by the raspberry pi firmware rather than the supervisor
Are you sure? I guessed the blinks were coming from the Balena supervisor since it matches the pattern described here and also occurs in the right circumstances, i.e. if I interrupt the internet connection. Also, the blinking ACT LED isn’t documented in the Pi docs here.
Are you positive that after you commented out the led file from /etc/resin-supervisor/supervisor.conf then you did not see the interference anymore?
If I comment out that line in supervisor.conf to say
#LED_FILE=<whatever>
I still get the interference. To stop the interference, I have to explicitly set it to
LED_FILE=/dev/null
Furthermore if I set it to
LED_FILE=/sys/class/leds/led1/brightness
Then the red PWR LED starts flashing in the Balena pattern when internet connection is lost, rather than the green ACT LED. This seems consistent with the Balena supervisor controlling the LED.