If I change the plane (or box as in your example) this doesn’t work anymore. This is actually what I’m trying to cut here, I added a plane in the example to make it easier to follow.
From my understanding, if I can manage to add the 0.01 in thinkness to the corrugated plane, then it would be fine (the thickness in the end result doesn’t bother me), but I’m unsure if I can extrude the mesh further, on the y axis.