So each unique message should have a unique identifier? If I just leave it as "required" then the game will think they're all the same message, or something? Or is it solely for the plugin to reference messages internally?
Yes, the plugin uses this information to reference its windows. I would say, each unique "window" should have its unique identifier. Just have a look at how RPG Maker handles Pictures, there you always need to pick a number from 1-50. It's the same here.