Chances are only the ALP engineers who developed the thing knows what the on-board headers are used for. Probably for the initial flash of the bootloader/serial/encryption keys and maybe for QA testing as well (test all the functions of the board before it's shipped). It may also be used for diagnostic purposes if a defective unit is sent back for repair/refurbishment. Even if it is an ICSP header, it's possible and probable that AL uses their own pinout rather than the standard one PIC programmers use. It could just be a diagnostic serial port to allow a diagnostic computer to talk to the processors on the board.
It's possible that the chips have bootloaders flashed on them even before they're installed on the board (I think Microchip offers this as a service for volume customers). They would still need serial #/encryption key info added if it's unique to each device. There's probably a computer at the factory programmed to do this, each time a board/CPU goes out it connects to the header, gives it a serial # and key, and prints the S/N stickers to put on the outside.
There's another header on the board, near the USB port. It's 6 pads inline but without holes. It looks much like a standard PIC ICSP header. And it even appears that pin 3 is ground and pin 6 is unused.
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