Sunlight has nothing to do with the yellowing process going on with things like the SuperNes and most older computer hardware. Plenty of people have reported it happening to items in their original packaging stored away, happening to the plastic from the inside as well as the exterior while if you broke the plastic it's still normal inside, etc.
It's the fire retardant causing it.
I always assumed so. But I can't give a definitive answer.
I don't know so I couldn't say. I only own two SuperNes consoles, my original and one of the redesigned models in the last day's of the console's lifespan to act as a spare. So I haven't experienced it first hand beyond the discoloration of the controller port area.
But your hypothesis seems to make sense if it wasn't always that way if you're the original owner of it. If you just picked it up and are wondering if it's going to start yellowing due to what you've noticed, I wouldn't worry. It could just as easily be that both halves of your console are from different manufacturing runs which could account for the slight variation in the coloring of both halves.