When generating a new superflat world with a custom preset set to "3;minecraft:air" and enabling structures, then the villages generated don't have gravel roads. It is not possible that the gravel fell down for two reasons: 1) the gravel doesn't update automatically, for example when generating a world with one layer of sand it doesn't fall down; 2) the villages generate with cobblestone under the gravel, meaning it can't physically fall down.