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>>This seems like a fairly simple question... nobody?
Yet you're asking it.
The example has NPCS2 as a NC, but it's just that, an example. The documentation also details how to use it with up to 15 SPI peripherals using an external 4-to-16 decode (0x0F is all deselected pattern) using a binary form. The Linux guys drive the SPI's CS's as soft GPIO's because the Atmel SPI implementation can be quite problematic for some devices, and is not uniform across all the families. Using GPIOs also allows a large number of devices to be used, and a flexible selection of pins.
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