A few thoughts:
First, the recipe calls for the addition of 1.5 oz. chocolate extract to the secondary. I don't know what effect that will have (is the extract clear, black, what?).
Second, "three days in" you see a lot of yeast, which lightens the color considerably. It will darken when the yeast drops.
Third, I don't know, how did you do the steep? Where did the grains come from? How was the crush? The stout in my sig was a little heavier on the roasted barley, not much though. It came out black black black.
Fourth, your boil is not the problem. You boil off water, not color. So you add more makeup water, it all evens out.
I would say, let it go and enjoy the beer when it's done. You'll have pleny of time to ponder, over a brew or three, what to do on your next batch.