I know a lot about fish, but I'm not a betta expert. However, I do think it's normal for them to look lighter or darker at times. My African cichlids are blue and one of them gets so dark sometimes she looks black. Do you see worms/parasites, spots, or damaged fins? Those are definite signs of disease.

Does the stress coat also remove chlorine and ammonia from the water? Is the betta eating? Is the filter gentle enough for bettas? Bettas are not strong swimmers and a filter that is too powerful will cause them a lot of stress.