Maybe the "onboard linux" is an RPi?
Early KNC indicate the host would be a embedded sodimm board so not a RPi. Then again it doesn't really matter. The host is relatively low end stuff. It needs a tiny amount of memory, a low end processor, ethernet, and some sort of serial connectivity to the ASIC boards. An embedded linux board will work fine, so will a RPi. I assume they simply have more experience with this board so they are using it.