I am using the Peggy2 board and it does connect Atmega Pin 2 (PD0) and Pin 3 (PD1) to 74HC154. I cannot change this since it is a PCB. The board has a jumper option to enable serial comm but I did not install that jumper.
The Peggy2 board does work with the programs and libraries written for it, but has the behaviour regarding the DataSheet truth table as mentioned.