So I decided not to use a skylight and instead opted for a very bright light with a large radius and fall off around the area where the sun is positioned on the sky-dome, this provides reasonably realistic lighting and does not have the same problems that the skylight was presenting.
I've had much difficulty creating the canyon for the flight stage, creating it both deep enough to look realistic, but shaped so that the light can reach the base and there are no areas where the player could get stuck, has proven difficult.