A number of GPIO pins between 2 and 31 have different possible applications. For example, GPIO8 can be connected to a signal wire for Serial GPIO, or it can be connected to a LAN port activity indicator, or it can be a manually controlled GPIO.
How it is configured depends significantly on how the specific board is wired. If in this example the board has Serial GPIO, then the physical pin will be wired to a 74HC595 or 74HC164 shift register chip, and the Serial GPIO configuration is the only one that makes sense.
However, if the board does not have Serial GPIO, then the physical pin is most likely wired to an LED, and the software may at times want to let that LED blink whenever there is activity on LAN port 2, and at other times the software may want to control that LED manually using the GPIO subsystem. The PINMUX allows for these configurations.
The GPIO pins and their possible functions are as follows:
For boards which use a 74HC595 or 74HC164 shift register chip to expose an additional 17 GPIO outputs using only 2 (or 3) pins on the main chip.
Output a timing reference from your choice three network subsystems.
If PCIe exists on the board, GPIO31 is wired as the slot 1 reset line.
If PCIe exists on the board, GPIO30 is wired to the slot 0 reset line.
If the SPI Flash Controller is wired to the flash chip for quad mode, lines 3 and 10 are used in addition to the normal SPI lines.
A second UART port is available, boards implementing this will use lines 3 and 10.
Devices with EPON/GPON will use lines 16-20 to communicate with the PON subsystem.
Devices with 2 VoIP phone jacks will use lines 4-7 to communicate with the 2nd VoIP subsystem.
Devices with a VoIP phone jack will use lines 12-15 to communicate with the VoIP subsystem.
The PCM subsystem contains an SPI interface that is used for communicating with SLIC chips such as Le9641 when in PCM-SPI mode. In principle, it can also be connected to any other type of SPI device. When enabled, it uses GPIOs 4-7. In ZSI mode, this is not necessary because control traffic is interleaved with PCM data.
Line 3 can be connected to the SLIC subsystem to receive an interrupt when the SLIC has something to communicate, it avoids the need for polling.
For devices with a VoIP phone jack, pin 2 can be wired to the reset pin on the SLIC chip.
This is probably the 3rd chip select line for the PCM SPI subsystem, with CS1 referring to the chip select line for the SPI Flash Controller.
For boards has 2 VoIP phone jacks using SLIC-SPI mode, this chip select line allows enabling the 3nd SLIC chip for SPI communication.
If line 3 is wired to an LED light, it can be connected to the activity meter for LAN Port 4. This is one pin which makes sense to configure at runtime, for example when switching an LED between showing network activity, and manually controlling it to display a pattern e.g. during startup or software update.
Activity indicator for LAN port 3
Activity indicator for LAN port 2
Activity indicator for LAN port 1
Activity indicator for LAN port 0
This doesn't occupy any known GPIO pins, it seems to change the output of the I2C subsystem, making it communicate with the xPON subsystem rather than the standard I2C output pins.