The mod can't edit a surface until after it's created. I'm not sure it's possible. If it's possible I'll add it eventually.
The settings from initial map creation are stored in game.default_map_gen_settings, which is read-only. They're used to create new planets. Only after creating the new planet is its data in a place that can be modified.
Maybe by listening to events, I could interfere with the creation of the surface and have it use modified settings. (I'm guessing and haven't researched this.) This might be too weird to bother with. It may be simpler to delete every chunk on the planet and let it regenerate, compared to trying to modify read-only settings before they can be used.
If you edited Gleba settings on another surface, you may have added Gleba water to that surface. I would not check unchecked boxes on a surface unless you're trying to add weird things on purpose.
I will try to think of a way to make this clearer. Perhaps the UI should say the name of the surface it's editing at the top, to make it clear you're editing one planet at a time, not global settings.