(Part Two) I like to think that just by being around each other, Lily and James started to change DUE to each other, by learning from each other - they say iron sharpens iron and friction caused by conflict between James/Lily is going to show each them things about themselves they didn't know - and then (hopefully) change, if it's needed. That's my view on it anyway :D
I think you definitely have something with the for/because distinction, but mostly simply because of the timing implied with the words. For me, "for" implies that they were "changing" before they had any kind of relationship. "Because" implies after. I think it would be ludicrous to say that after James and Lily became involved, they stayed exactly the same. Of course not. When personalities mesh, you often have give and takes. You're exposed to new things. That's what being in a relationship is about.
I suppose my major issue with the "change" phenomenon is actually due in large part to the timing and the motivation that's implied with "James changed for Lily/Lily changed for James." Because like you said, changing yourself for someone (pre-relationship, bending entirely to their whim) is unhealthy. Changing because of someone (during relationship, because with the entrance of them, you're life is inevitably changing) is natural. So you do have very good points. I'm being too broad when I say I get sickened over the concept entirely. I don't think Lily or James changing during their relationship--or even pre-relationship, when they are interacting substantially--is wrong. But when people say "James changed for Lily," I don't think they're usually talking about that. I think they're talking about before Lily even gave James the time of day, with her as the catalyst for his "grand transformation."