Long story short, they're for flags which are used for tracking choices, met characters, visited places, certain conditions used for unlocking scenes, etc. Debug mode not only can list them, but also allows to set them manually but these functions won't really give anything to end user as they exist primarily for development purposes. The things that are more useful for end user is the ability to play any scene you want (if you know their code name), tracking / setting affection points and skill points or changing size. Bear in mind though that messing with it can lead to errors if you don't know what you're doing