Although hierarchical layout supports layering constraints, yEd does not provide a way to specify such constraints.
The only thing that comes close is "Layers" -> "Layer Assignment" set to "From Sketch". First run the algorithm with any other "Layer Assignment". Then manually move the nodes you want to constrain to the same y-coordinate. yEd's snap lines should make it fairly easy to do so. Finally, choose "From Sketch" and run the algorithm once more.