If you remove all layers in the superflat world generator, it will reset to the default when you click "done".
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"empty layers are filled with air". Exactly. The superflat world generator replaces all empty layers with air, except when they are all air. This inconsistent behavior makes me pretty sure that it isn't intended.
I'm not editing the text input, I'm just selecting a layer and clicking "remove layer", until all the layers are gone.
This is intended. The generator has to know wich blocks it should create. When all the layers are deleted, then the generator has no information and so no input.
To solve it, make layers with Air and it should work. Go to presets and type in the upper box 3;air.
No it's not. The generator automatically replaces empty layers with air. So a world with the preset "1 layer of bedrock", will be generated as 1 layer of bedrock, and 255 layers of air. The same thing should happen with the an empty preset. The generator should do what it does with other worlds, and replace all empty layers with air, resulting in 256 layers of air. But it doesn't.
Additionally, if this behavior were intended, then the "done" button would become grayed out when there are no layers chosen. Instead, it appears to work, but then resets without informing you. This is clearly buggy behavior.
I suspect this is intended, as even empty layers are filled with air. Using 1 layer of air and nothing else works fine in generating an empty world.