I always assumed it was due to the light pollution reflecting off the clouds from Rupture Farms. I mean, check this out:
(source)
Also if you splice those images together without the border lines, with them zoomed out, it's easy to see the rainbow. It's not really something you notice when you play the game screen by screen - It really amazed me when I tried splicing those screens together (before I found the image STM posted). I hope this is retained in the new version.
