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While I don't know why, I have been doing a lot of digging through the Linux kernel support for the Quark lately. The SPI driver uses GPIO functions for the SS pins so it is done through software rather than a hardware controller. The advantage of doing it in the driver instead of Arduino programs is that it should be faster due to fewer kernel calls. The kernel also uses the native CPU GPIO instead of the IO extender. So it seems to me that taking advantage of the driver would make more sense. I too am surprised by the choice.