When I try to use a structure  block in a superflat world with caves and cliffs  experimental feature  on, the Y level always jumps up as high as it needs to reach Y=0. If I try to to change it back to below Y=0, it goes back to Y=0. I have only tried it while the structure block was below Y=0. I think if you add the new caves and cliffs Y level range to the structure block's range that should fix it.