I'm running a custom firmware on the ATmega16U2 (Switch-Fightstick). Is it possible to access the digital pins of the UNO from the ATmega16U2?
No, only the ATmega328P has access to the external pins of the Uno. You would need to write code for both the '328P and the '16U2 to communicate the pin values and changes over serial since that is the only channel connecting the MCUs.
There is a 4-pin header JP2 on the board that brings out the following pins from the '16U2
PB4, PB5, PB6, PB7
and the ICSP connector
PB1, PB2, PB3
Thank you for letting me know, although the accepted answer better suits my question. It's a bit of a hassle though that they are filled with solder by default on the UNO...– skiilaaDec 31, 2017 at 11:53