FPGA pins P8, T8, and M7 are routed in the PCB to Raspberry Pi GPIO pins 16, 20, and 21 but those Raspberry Pi pins are not exposed/used anywhere unless you specifically do so in the FPGA code.
For example, in this FPGA code modification example, Raspberry Pi GPIO16 is routed through FPGA P8 pin to MATRIX Voice expansion GPIO 15 through FPGA pin R2. This allows direct access to RPi GPIO16 even though the pin itself is used up by the MATRIX Voice.
Are you trying to do something like the above example?
Let me know if that helps you in any way and if not, it would be great if you could expand a bit on what you are trying to do so we can help more effectively!