For the first time, appanah, with all due respect I disliked your analysis. It's not that I disagree of it; rather, I disapprove of it. Before I begin my argument, I want to make it clear that I don't want to offend you and hope you'll continue posting them.
That said, I think you've dug too deeply into this episode. If the butterfly effect happened in this episode, there are a number of different episodes---nearly every episode--in which this theory could have played a large role. Take Billboard; if one little thing had changed, the boys wouldn't be sitting atop that billboard. I don't think that we need to make that connection merely because the name of the episode happens to be butterflies.
Unlike some of the past episodes, this one has tried to be a bit funnier than the last. I'm not saying episodes like Ida Loses a Leg weren't funny, because it was, but in a different way. I sincerely feel that the premise behind the butterflies was meant to be sheer funniness rather than part of an elaborate scheme; however I am impressed you counted the number of seconds the butterflies were on-screen.
Furthermore, to be perfectly honest, I think that the chrysilis theory for the man at the Lucky Aide is just goofy. When he goes under the shelves, he has already completed his transformation; he's not in the midst of it. The man is very helpful to some, but he's a hazard that doesn't follow the rules to others, and no matter how good these rule-breakers are, they need to be punished for breaking the rules. Even if the rules are being broken for a good purpose, they are still being broken, and if you go about breaking the rules, then there's really no point in having them in the first place, is there?
It was an interesting change for Reese, but we've seen it before. Reese has always had an odd soft side for animals. Take Vegas, when he became obsessed with his rabbit, and put his heart and soul, even his finger, into keeping it alive and making it fatter. This is merely a character trait of Reese, not a transformation, as you suggested.
I really enjoyed this episode, but I do not believe it conveyed the amount of symbolism you inferred.