Thanks for the provided scene. That's caused by features working with area "edges" - like the Falloff feature and the Edge Boundary Checking mode. If you need to enable these, using the UV mode would be recommendable. If that's not necessary, using the Point Boundary Checking mode and disabling the Falloff feature (using Material IDs might be an option) will allow using these "stacked surfaces" in the XY mode.
I hope that clears it up and in case of any further question(s) or doubt(s), please don't hesitate to contact us. Have a nice week.