I have this theory about Harmonizing Alters in S-CRY-ed, I think they represent independence. Only two characters acually use harmonizing alters during the series, Kazuma and Straight Cougar. The rest use alters that manifest as seperate entities, and also they each show personalities that suggest feelings of being outcasts and/or a desire to join a group, so it seems like they use their alters to create companions when they are alone. Kazuma is unique because he doesn't feel he needs anybody; he cares about his friends, but he seems to feel they need him more than he needs them, thus his alter manifest as a part of him because he just needs himself to be stronger rather than getting help from an independent alter. Straight Cougar uses an independent alter when he's with HOLY, but then switches to a harmonizing alter when he goes rogue near the end of the series, symbolizing his part of the group dynamic with the independent alter as a part of HOLY, then his independence with the harmonizing alter.

Any thoughts?