The reason for the reverse photo-period is that photosynthetically active algae produces O2 and consumes CO2... This raises the O2 level, but also keeps the pH from dropping as much at night...
When your main tank is lit, the corals and algae in it are performing this function, so if you don't take some other action, your pH can take a drastic dive during the main tank's lights out. If your refuguim is lit opposite (Or longer) than the main tank, this helps soften the pH dive when the main lights go out on your main tank...