So i tried to generate Lost cities on a super flat world, the world contains 50 minecraft:stone layers so i dont think is a problem with the depth of the world.After creating the custom preset of a super flat world, i go to LC generation settings and i select onlycities, when i load the world is just a flat world, without any city on it.

Superflat is a very special type of world generation. I don't think it supports modded structures