When I was in FTC a few years ago, "stock software" referred to both the software on the laptop and the software on the robot. In particular, I recall Linux on the laptop wasn't a supported OS for any of the allowed programming environments (LabView and RobotC).
Right, what I mean is that they can only run programs (and communicate with the robot) in the Lego Mindstorms drag and drop language (which is actually decent). If we could have someone with an Xbox controller in the bleachers somewhere that would be cheating.
I've organized a Mini Nodecopter event in London and another is on this weekend in Bath, UK. They are, in my experience, some of the most exciting hackdays I've been too, bringing software and hardware hacking together to command flying robots!