We wanted to be able to put both 100-pin and 144-pin components on the board, so we designed the board as shown in the attached document.
I ran a pattern through the pins that had the equivalent functions of the 100-pin and 144-pin components, and dropped all unused pins of the 144-pin ones to ground.
This prototype board uses the 144-pin one, and the firmware is the program that was used when the 100-pin one was used.