Typically, APM/MavLink runs on a Arduino (my Quanum CX-20 quad runs an Mega 2650). This looks like this is a Raspberry Pi shield that I suspect contains an ATmega - so it's not Linux that is doing the flight controlling.
Actually we run APM code ported to Linux, there is no Atmega on the board. There was a lot done to make this possible including special real-time Raspbian. It flies very stable and with great timing performance.