Instead of first creating the arrangement of the four rectangles, duplicating them along the Z-axis, and then deleting individual instances, you could build it up a little more refined and thus enable more precise control.
If you first duplicate a rectangle (in this case, I use the node Curve Circle
with four points) along the Z-axis and then instantiate the objects in the desired arrangement at these points, you can decide directly at each point whether a rectangle should be created at all or not.
It would look something like this:
(Blender 4.2.0+)
If you also want to alternate the rotation of the individual layers, you can easily extend this setup by using index and modulo to give every other layer a different rotation: