Again, I totally get where you're coming from on this; it's just that that direction just doesn't feel at all satisfactory from a story angle, moderating factors or no. Take basically any of the changed characters as an example: if, say, Lilly's whole plot has been her coming to terms with the idea of being like this for the rest of her life, and she's finally moving towards acceptance, what does it do to that story arc to have it suddenly end with her being able to become a middle-school boy again? It basically undoes her entire plot. Same for a lot of the other characters; if the huge, life-impacting event they've spent months dealing with is suddenly a strictly opt-in affair, then the whole thing just feels like one long shaggy-dog story.
That's basically my feelings on the issue, and since I can think of a couple in-universe justifications for that stance, I ran with it in the chapter. Again, I completely understand your reasoning, I just can't really get over the fact that it makes a whole lot of the story feel pretty much pointless.