Good point. +1 
I feel this is worth fixing the core, but I don't know where to write this.
I shall call to @pert
Specifically, add two NOT_A_PIN to the end of the array below.
https://github.com/arduino/ArduinoCore-avr/blob/master/variants/standard/pins_arduino.h#L150
As long as A6 and A7 are defined, they should also be present in the array.
https://github.com/arduino/ArduinoCore-avr/blob/master/variants/standard/pins_arduino.h#L62
https://github.com/arduino/ArduinoCore-avr/blob/master/variants/standard/pins_arduino.h#L71
The pinMode function ignores from port-arrays whose data is NOT_A_PIN.
https://github.com/arduino/ArduinoCore-avr/blob/master/cores/arduino/wiring_digital.c#L35