I am using a RPi 3 with a 4 amp power supply. You made the claim that you can use only one hat per the spec. Where can i find a copy? Adafruit and others talk about many hats stacked on top of the Pi.
The ID eprom poses an interesting question. If the Pi software during boot looks at some of the GPIO pins to determine what hats are present, then i can see possible conflicts.
It appears that the Automation hat uses the ID over the I2C pins as the Pi and software do detect it correctly. I was able to control the relays, Analog and in and out ports on the Automation hat with only the terminals on it and the power and I2C pins connected with jumper wires. The Servo hat also works when connected this way.