This is my hypothesis.
They made the three main episodes, added post-game content (the extra bosses, etc) and then belatedly realized that only Aqua was playable in the Final Episode, so a band-aid fix was to bump the other two's combat levels in their game-clear saves, since they did not have a final episode.
That would mean that by design Aqua would never have a bumped combat level in her normal game-clear save, since Final Episode was meant to be her post-game.
That band-aid hypothesis would probably also explain why the implementation itself was so shoddy and prone to glitching out under very reproducible, specific circumstances (which the logic fails to account for, e.g. multiple game clear saves, or re-clearing the other characters after unlocking and beating Final Episode, etc)