So this doesn't do anything.... I'm pretty sure this script doesn't get called until you actually program the mcu... and I believe the pins get reset by the omega after the script runs.
I think the issue here is I'm holding my radio IC's Chip Select pin high (to communicate with it from the arduino) and at the same time the omega is also trying to use the bus, since these two are connected and since the omega uses the spi bus to communicate with flash memory there is really no way to turn it off, with the omega still remaining useful.
I could be wrong but from all the tests I've done this seems to be the case. It just seems odd that they would break these pins out when they are totally useless on the arduino side.